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Genetik

Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform

Published: August 17, 2022
doi:
10.3791/63493
, , , , , , , , , , , ,
1Centre for Women, Children, and Reproduction,Guangxi Key Laboratory of Metabolic Diseases Research, 2Department of Biopharmaceutics, School of Laboratory Medicine and Biotechnology,Southern Medical University, 3Department of Obstetrics and Gynecology,Chinese PLA General Hospital, 4Clinical Laboratory,Northern Theater Air Force Hospital, 5Guangzhou Darui Reproduction Technology Co., Ltd.

Özet

The protocol presents the overall in-lab procedures required in pre-implantation genetic testing for aneuploidy on a semiconductor-based next-generation sequencing platform. Here we present the detailed steps of whole genome amplification, DNA fragment selection, library construction, template preparation, and sequencing working flow with representative results.

Abstract

Next-generation sequencing has gained increasing importance in the clinical application in the determination of genetic variants. In the pre-implantation genetic test, this technique has its unique advantages in scalability, throughput, and cost. For the pre-implantation genetic test for aneuploidy analysis, the semiconductor-based next-generation sequencing (NGS) system presented here provides a comprehensive approach to determine structural genetic variants at a minimum resolution of 8 Mb. From sample acquisition to the final report, the working process requires multiple steps with close adherence to protocols. Since various critical steps could determine the outcome of amplification, quality of the library, coverage of reads, and output of data, descriptive information with visual demonstration other than words could offer more detail to the operation and manipulation, which may have a great impact on the results of all critical steps. The methods presented herein will display the procedures involved in whole genome amplification (WGA) of biopsied Trophectoderm (TE) cells, genomic library construction, sequencer management, and finally, generating copy number variants’ reports.

Introduction

Aneuploidy is the abnormality in the number of chromosomes by the presence of one or more extra chromosomes or the absence of one or more chromosomes. Embryos that carry some type of aneuploidy, such as the loss of one X chromosome (Turner syndrome), extra copies of autosomes, like trisomies of autosome 21 (Down syndrome), 13 (Patau syndrome), and 18 (Edwards syndrome), or extra sex chromosomes such as 47, XXY (Klinefelter syndrome) and 47, XXX (Triple X syndrome), can survive to term with birth defects1. Aneuploidy is the primary cause of first trimester miscarriages and in vitro fertilization (IVF) failure2. It is reported that the aneuploidy rate could range from 25.4%-84.5% through the different age layers of the natural cycle and medicated control group in IVF practice3.

Next-generation sequencing technology is becoming wildly applied in the determination of genetic information clinically; it provides practical access to genome sequence with efficiency and high throughput. Particularly, next-generation sequencing also revolutionized the diagnosis of disorders with genetic factors and tests for abnormity in the genome4. Using semiconductor sequencing technology to directly transfer chemical signals in sequencing bio-reaction into digital data, the semiconductor-based sequence system provides a direct, real-time detection to sequence data in 3-7 h5,6.

In an IVF procedure, pre-implantation genetic testing (PGT) investigates the genetic profile of the embryo before being transferred into the uterus to improve the IVF outcome and reduce the risk of genetic disorders in newborns1,7. In PGT combined with NGS techniques, genetic material extracted from less than 10 cells is amplified with whole genome amplification kits or an independently developed whole genome amplification reagent. This requires only one step in the amplification phase and does not require pre-amplification, to obtain whole-genome amplification products. Primers or panels for copy number variant and special gene loci sequencing are designed and applied in the library constructed.

A typical workflow of pre-implantation genetic testing-aneuploidy (PGT-A) in NGS involves serial procedures, and requires an intense workload of laboratory personnel8. Some misoperation caused procedure roll-back may lead to undesired loss of both time and resources of the lab. A concise and clear standard operating procedure (SOP) for PGS-NGS workflow is helpful; however, word-format protocols cannot present more detailed information on sample processing, device manipulation, and instruments’ settings, which can be visualized in a video protocol. In this article, a validated workflow combined with a visualized demonstration of operating detail could offer more direct and intuitive referring protocols in PGT practice on a semiconductor sequencing platform.

The protocol here describes a method that supports batching up to 16 embryo biopsies in parallel. For larger batches, it is recommended to use a commercial kit-based protocol for semiconductor sequencing, such as Reproes-PGS.

Protocol

All protocols and the trophectoderm (TE) biopsy (1.1.1.1 section) applied in this study were reviewed and approved by the human research ethics committee of No. 924 hospital on September 18th, 2017 (NO: PLA924-2017-59). The patients/participants provided their written informed consent to participate in this study.

1. DNA isolation from human embryo biopsy and whole genomic amplification

  1. Protocol for whole genome amplification9,10
    NOTE: Pico PLEX WGA Kit is used to perform whole genome amplification.
    1. Sample collection and storage
      1. Trophectoderm biopsy: Draw on an average of six to nine cells from herniated TE of D5/6 embryo after assisted hatching to obtain a qualified amount of DNA for the following amplification.
      2. Transfer the sample cells to a PCR tube in 5 µL of PBS.
      3. Immediately freeze the samples at -80 °C if the protocol does not directly proceed to the DNA extraction.
    2. Cell lysis
      NOTE: Supplementary File 1 lists and serves as a reference for the recommended volumes of each component when preparing the master mix during cell lysis and whole genome amplification of batches of 1, 8, 16, and 32 samples (with overage to accommodate pipetting errors). When formulating other master mixes of this protocol, the volume of each component is additionally increased to accommodate the component consumption caused by repeated pipetting. All brief centrifugation is performed on a tabletop mini centrifuge for 2-10 s at room temperature (RT), with a fixed RPM of 10,000 with a centrifugal force of 5,300 x g. The centrifugal force must be between 2,000 x g and 12,000 x g.
      1. Prepare the cell lysis mix with 4.8 µL of the extraction enzyme dilution buffer and 0.2 µL of the cell extraction enzyme per sample.
      2. Pipette 5 µL of the freshly-prepared cell lysis mix into each 5 µL cell sample in PCR tubes, and briefly centrifuge the tube at RT for 5 s. Do not vortex the tube.
      3. Incubate the sample in a thermal cycler as follows: 75 °C, 10 min; 95 °C, 4 min; 25 °C, 14 min. Briefly centrifuge (5 s) the tube after the incubation.
    3. Pre-amplification of the whole genome DNA
      1. Prepare the pre-amplification mix with 4.8 µL of the pre-amp buffer and 0.2 µL of the pre-amp enzyme per sample.
      2. Pipette 5 µL of the pre-amplification mix into the sample tubes through the walls of the tube, and briefly centrifuge for 3 s. Avoid the tip reaching the bottom of the tube, and do not vortex the tube.
      3. Incubate the sample according to the thermal cycler program mentioned in Table 1.
    4. Whole-genome DNA amplification
      1. Briefly centrifuge the sample for 5 s and place the pre-amp incubation product on ice.
      2. Prepare the whole genome amplification mix with 25 µL of the amplification buffer, 0.8 µL of the amplification enzyme, and 34.2 µL of nuclease-free water per sample.
      3. Mix 60 µL of the freshly prepared whole genome amplification mix with the 15 µL of pre-amp incubation product; the total volume needs to be 75 µL. Briefly centrifuge for 5 s. Avoid the tip reaching the bottom of the tube, and do not vortex the tube.
      4. Place the PCR tube on the thermal cycler and run the thermal cycler program mentioned in Table 2.
      5. Centrifuge the tubes briefly for 5 s and transfer the products into a new 1.5 mL centrifuge tube.
      6. Quantify the WGA product concentration with a fluorometer11. Samples can be temporally stored at -20°Cfor less than 2 months if not proceeded to the next step.
  2. Protocol of the independently developed WGA reagents.
    1. Sample collection and storage
      1. Draw the cells from the D5/6 embryo after assisted hatching for the following amplification.
      2. Transfer the sample cells with 1.5 µL of PBS into a PCR tube containing 2 µL of PBS.
        NOTE: PBS is free of Mg2+ and Ca2+.
      3. Freeze the samples immediately at -80 °C if not directly proceeded to the DNA extraction protocol.
    2. Cell lysis
      1. Melt the cell lysis buffer (40 mM Tris (pH 8), 100 mM NaCl, 2 mM EDTA, 1 mM ethylene glycol tetraacetic acid (EGTA), 1% (v/v) Triton X-100, 5 mM sodium pyrophosphate, 2 mM β-glycerophosphate, 0.1% SDS) at RT and place it on the ice. Add 2 µL of cell lysis buffer to each sample, and centrifuge briefly (5 s).
        NOTE: Do not vortex the tube, and avoid the pipette tip touching the liquid surface in the tube to avoid bringing cells or DNA out of the reaction system.
      2. Incubate the sample in a thermal cycler as follows: 55 °C, 20 min; 95 °C, 10 min; 4 °C, hold. Briefly centrifuge the tube at RT for 10 s after the incubation.
    3. Whole-genome DNA amplification
      1. Briefly centrifuge the cell lysis product for 5 s and place it on ice.
      2. Prepare the whole genome amplification mixture for each sample by mixing with 16 µL of amplification pre-mixed solution, 1 µL of amplification enzyme, and 28 µL of nuclease-free water. Mix gently, centrifuge briefly (5 s), and place the mixture on ice. Do not vortex the tube.
      3. Pipette 45 µL of the freshly prepared whole genome amplification mixture into the cell lysis product prepared in step 1.2.2.2; mix gently and centrifuge briefly for 5 s.
        NOTE: Do not vortex the tube and avoid the pipette tip touching the liquid in the tube.
      4. Place the PCR tube on the thermal cycler and run the program as detailed in Table 3.
      5. Centrifuge the tubes shortly for 5 s and transfer the products into a new 1.5 mL centrifuge tube.
      6. Quantify the WGA product concentration with a fluorometer11 and record the results on the QA (quality analysis) sheet. Products with qualified concentrations can be temporally stored at -20 °C for less than 2 months if not proceeded to the next step.

2. Amplification fragment selection

NOTE: Materials used in this section are available in the Library Preparation Kit (Table of Materials).

  1. Preparation before starting
    1. Equilibrate the magnetic beads (n x 100 µL) for purification at RT for 30 min.
    2. Restore the previous WGA product to RT. Vortex the product at RT for 30 s before centrifuging it briefly.
    3. Prepare fresh 70% ethanol.
  2. Fragment selection procedure
    1. Pipette 25 µL of the WGA products and transfer into a 1.5 mL centrifuge tube with 25 µL of nuclease-free water preloaded.
    2. Vortex and mix the DNA purification beads well. Aliquot 50 µL of it into each sample tube (original sample: beads (volume) = 1:1), vortex, and centrifuge briefly (5 s). Set the tube for 5 min at RT for the DNA binding process.
    3. Insert the 1.5 mL centrifuge tube into a magnet rack, and wait till all the magnetic beads are attracted to the sidewall of the tube. Carefully transfer the supernatant into a new 1.5 mL centrifuge tube. Avoid pipetting the beads out.
    4. According to the original sample volume, pipette 30 µL (original sample: beads (volume) = 1:0.6) of magnetic beads, vortex, and centrifuge briefly (5 s). Set the tube for 5 min at RT for the DNA binding process.
    5. Insert the 1.5 mL centrifuge tubes into the magnet rack, and wait for 5 min till all the magnetic beads are attracted to the sidewall of the tube. Carefully remove and discard the supernatant. Avoid pipetting the beads out.
    6. Pipette 300 µL of 70% ethanol into the 1.5 mL centrifuge tube, gently rotate the tube twice with a 180° angle, and move the beads along the tube wall for a thorough wash. Pipette and discard the supernatant. Avoid pipetting the beads out.
    7. Repeat the wash procedure once.
    8. Remove the 1.5 mL centrifuge tube from the magnet rack and centrifuge shortly (5 s). Insert the tubes back into the magnet rack, and wait till all the magnetic beads are attracted to the sidewall of the tube.
    9. Carefully pipette out the remaining liquid at the bottom. Keep the tube open to dry the beads at RT for 3-5 min. Keep moisture off the beads.
      NOTE: Close the lid immediately if any cracks emerge on the pellet of beads.
    10. Remove the tubes from the magnetic rack, pipette 25-30 µL of the DNA elution buffer into a tube, and close the cap and vortex. Centrifuge briefly (5 s) to get the turbid liquid to the bottom of the tube, and set the tube at RT for 5 min.
    11. Insert the tubes back into the magnetic racks, and wait till all the beads are attracted to the tube sidewall and the supernatant turns transparent. Carefully transfer the DNA solution into new 1.5 mL centrifuge tubes. Avoid pipetting the beads out.
    12. Quantify the concentration of DNA after fragment selection with a fluorometer11, store it at -20°C. Typically, the concentration of the DNA fragment selected ranges from 1.5-2.4 ng/µL.

3. Preparation of the DNA library12

NOTE: Materials used in this section are available in the Library Preparation Kit (Table of Materials).

  1. End repairing
    1. Equilibrate the magnetic beads at RT for 30 min.
    2. Equilibrate the DNA product of fragment selection in step 2.2.12 to RT. Check and record the tag on each vial containing the DNA.
    3. Prepare the DNA end-repair system with 30 µL of DNA products, 10 µL of end repairing buffer, 0.5 µL of end repairing enzyme, and 9.5 µL of nuclease-free water in a 1.5 mL centrifuge tube. Vortex the tube for 30 s and centrifuge briefly (5 s) at RT to get all liquid to the tube bottom.
    4. Incubate at 25 °C for 30 min, and briefly centrifuge (5 s) the tube after incubation.
    5. Vortex or reverse-mix the magnetic beads, and transfer 75 µL of the magnetic beads into a tube containing end-repaired DNA samples (original sample: beads (volume) = 1:1.5). Pipette or gently vortex to mix the beads well and briefly centrifuge (5 s) to spin all the suspension down to the bottom of the tube. Set the tube for 5 min at RT for the DNA binding process. Flip the tubes gently to keep the beads dispersed.
    6. Insert the centrifuge tubes into the magnet rack, and wait for 5 min till all magnetic beads are attracted to the sidewall and the supernatant becomes transparent. Remove the supernatant, and avoid pipetting the beads out, keeping the tubes on the rack when pipetting.
    7. Transfer 300 µL of the newly prepared 70% ethanol into the tubes, gently rotate the tubes twice at a 180° angle, and move the beads along the tube wall for a thorough wash. Pipette and discard the supernatant. Avoid pipetting the beads out.
    8. Repeat the wash procedure once.
    9. Remove the 1.5 mL centrifuge tubes from the magnet rack, and centrifuge briefly (5 s). Insert the tubes back into the magnet rack, and wait for 5 min till all the magnetic beads are attracted to the sidewall of the tube.
    10. Carefully pipette out the remaining liquid in the bottom. Open the cap of 1.5 mL centrifuge tubes and dry the beads at RT for 3-5 min. Keep moisture off the beads.
      NOTE: Close the lid immediately if any cracks emerge on the pellet of beads.
    11. Pipette 33 µL of DNA elution buffer into a tube, close the cap, and vortex. Centrifuge briefly (5 s) to get the turbid suspension to the bottom of the tube and set the tube at RT for 5 min.
    12. Insert the tubes back into the magnetic racks, and wait till all the beads are attracted to the sidewall and the solution turns transparent. Carefully transfer the DNA solution into new 1.5 mL centrifuge tubes with the proper tag, avoiding pipetting the beads out.
  2. Barcode ligation
    1. Place the barcode ligation reagents in step 3.2.2 on ice to melt all the frozen reagents.
    2. Prepare the ligation system with 32 µL of end-repaired DNA products, 10 µL of nuclease-free water, 5 µL of ligase buffer, 1 µL of ligase, and 1 µL of P1 adapt in a 1.5 mL centrifuge tube. Pipette out 1 µL of each barcode reagent into the solution mix in the tube for one sample, vortex for 5 s, and centrifuge briefly (5 s) to get all liquid in the tube bottom.
      NOTE: When adding the barcodes, confirm that the number of barcodes and samples correspond; open only one barcode vial at each time to avoid the mixed pollution of barcodes; Change the gloves for every five or six barcodes added.
    3. Incubate the tubes at 25 °C for 30 min.
    4. Pipette 75 µL (original sample: beads (volume) = 1:1.5) of the magnetic beads into a tube, and pipette or gently vortex to mix the beads well. Centrifuge briefly (5 s) to spin all the suspension down to the bottom, avoiding bead aggregation. Set the tube for 5 min at RT for the DNA binding process. Gently flip the tubes to keep the beads dispersed.
    5. Insert the centrifuge tubes into the magnet rack, and wait for 5 min till all the magnetic beads are attracted to the sidewall and the supernatant becomes transparent. Remove the supernatant and avoid pipetting the beads out, keeping the tubes on the rack when pipetting.
    6. Transfer 300 µL of the newly prepared 70% ethanol into tubes, gently rotate the tubes twice at a 180° angle, and move the beads along the tube wall for a thorough wash. Pipette and discard the supernatant. Avoid pipetting the beads out.
    7. Repeat the wash procedure once.
    8. Remove the 1.5 mL centrifuge tubes from the magnet rack and centrifuge briefly (5 s). Insert the tubes back into the magnet rack and wait for 5 min till all magnetic beads are attracted to the sidewall of the tube. Carefully pipette out the remaining supernatant in the bottom.
    9. Keep the tube cap open to dry the beads at RT for 3-5 min. Keep moisture off the beads.
      NOTE: Close the lid immediately if any cracks emerge on the pellet of beads.
    10. Pipette 15 µL of the DNA elution buffer into the tube. Rinse the beads' pellet down to the bottom of the tube, seal the cap, and vortex. Centrifuge briefly (5 s) to get the turbid suspension to the bottom of the tube and keep the tube steady at RT for 5 min.
  3. Fragment amplification
    1. Place the library buildingreagents on ice when the frozen reagent dissolves.
    2. Transfer 47.5 µL of the enzyme mix and 2.5 µL of the primer mix into the tube containing eluted DNA and beads, vortex for 5 s, and centrifuge briefly (5 s) to get all liquid to the tube bottom.
    3. Set the tube at RT for 5 min. Insert the tubes back into magnetic racks, and wait till all beads are attracted to the sidewall and the supernatant turns transparent. Carefully transfer the DNA solution into 0.2 mL PCR tubes with tags marked clearly, and avoid pipetting the beads out.
    4. Incubate the sample in a thermal cycler set with the following program: 72°C, 20 min; 98 °C, 2 min; 98 °C, 15 s; 62 °C, 15 s; 70 °C, 1 min (6 cycles); 70 °C, 5 min. Briefly centrifuge (5 s) the tube when the reaction is finished and store the products at 4 °C.
    5. Transfer the PCR products into a 1.5 mL centrifuge tube (low attachment). Add 97.5 µL (original sample volume: beads (volume) = 1:1.5) of magnetic beads into the tube when the reaction ends, pipette or gently vortex to mix the beads well, and briefly centrifuge (5 s) to spin all liquid down to the bottom. Avoid beads aggregation. Set the tube at RT for 5 min. Gently flip the tubes to keep the beads dispersed.
    6. Insert the centrifuge tubes into the magnet rack, and wait for 5 min until all magnetic beads are attracted to the sidewall and the supernatant becomes transparent. Remove the supernatant, avoid pipetting the beads out, and keep the tubes steady on the rack.
    7. Transfer 300 µL of the newly prepared 70% ethanol into tubes, gently rotate the tubes twice at a 180° angle, and move the beads along the tube wall for a thorough wash. Pipette and discard the supernatant. Avoid pipetting the beads out.
    8. Repeat the wash procedure once.
    9. Remove the 1.5 mL centrifuge tube from the magnet rack and centrifuge briefly (5 s). Insert the tube back into the magnet rack, and wait for 5 min till all magnetic beads are attracted to the sidewall of the tube. Carefully pipette out the remaining liquid in the bottom.
    10. Keep the tube cap open to dry the beads at RT for 3-5 min. Keep moisture off the beads.
      NOTE: Close the lid immediately if any cracks emerge on the pellet of the beads.
    11. Pipette 22 µL of the DNA elution buffer into the tube, rinse the beads' pellet down, and close the cap and vortex. Centrifuge briefly (5 s) to get the turbid liquid to the bottom of the tube and set the tube at RT for 5 min.
    12. Quantify the concentration of constructed DNA library with a fluorometer11 and store the constructed DNA library at -20 °C; the concentration of the DNA fragment selected ranges from 0.6-10 ng/µL. Re-code the library information in the library database and store the samples accordingly.

4. Preparation of sequencing template13,14

NOTE: Materials used in this section are available in the Template Preparation Kit Set (Reagents/Solutions/Materials) of the Sequencing Reactions Universal Kit (Table of Materials).

  1. Library mix
    1. Fill in the form of a pre-run records sheet in the server system and tag the sample tube with library concentration and barcode number. Avoid using the same barcodes on different samples in one run.
    2. Vortex and mix the library sample, and centrifuge briefly (5 s). Dilute all the samples to 100 pM with nuclease-free water, vortex for 30 s, and briefly centrifuge the sample.
      NOTE: Given that DNA has a mean length of 260 bp, and 1 bp is 660 g/mol, calculate the conversion of ng/µL to pM using the following equation: 1 ng/µL = 5,827.5 pM/L.
    3. Pipette 10 µL of 100 pM diluted library into a 1.5 mL centrifuge tube, vortex for 30 s, and briefly centrifuge for 2 s. Keep the mixed library on ice.
  2. Template preparation
    1. Start the template amplification system and choose the clean program. Add the reaction oil to 1/2 of the tube, and add the emulsifier breaking solution to 1/3 of the tube.
    2. Confirm that the amplification plate and washing adapter are set in the ON position. Clean the waste bottle, and put a needle into a new 50 mL centrifuge tube to collect waste. Confirm the processed steps on the screen of the template amplification system. Press NEXT to start a clean program, which will take about 15 min.
    3. Replace the amplification plate with a new one after the clean program, insert the collection tubes containing 150 µL breaking solution II into the rotor, and place the bridge on the collection tubes. Add the reaction oil to 1/2 of the tube and the emulsifier breaking solution to 1/3 of the tube.
    4. Emulsify PCR reagent preparation: Equilibrate the emulsified PCR buffer at RT until it dissolves, briefly centrifuge (5 s) all reagents, and place them on ice before use.
    5. Pipette 120 µL of the emulsified PCR enzyme mix, 100 µL of template Ion Sphere Particle (ISPs) buffer, 170.5 µL of nuclease-free water, and 9.5 µL of the mixed library (100 pM) into a tube containing 2,000 µL of emulsified PCR buffer. Mix the solution well with repeated pipetting.
      NOTE: The mixed solution must be loaded on the template amplification system within 15 min; perform all procedures at RT.
    6. Place a new filter for template preparation steady on the tube rack with the sample portal upwards. Vortex the solution for 5 s, centrifuge briefly (5 s), and transfer the solution into the sample portal of the filter after repeatedly pipetting 800 µL three times. Centrifuge the tube to decrease bubbles before the last injection. Avoid injecting air into the filter. Inject 200 µL of reaction oil II following the mixed solution.
    7. Turn the sample portal of the filter downwards, and replace the washing adapt with the filter. Insert the sample needle into the center hole of the rotor lid and then press the needle to the bottom.
    8. Press the RUN button on the screen, choose the program according to the corresponding kit, and press ASSISTED to check all steps. Press NEXT till the run is started; it takes about 4.5 h to finish.
    9. Press NEXT when the program is finished; the system will start a 10 min centrifugation. When the centrifugation stops, press the Open Lid button and move the collection tubes to racks. If the procedure does not go to the next step in 15 min, press on Final Spin to re-centrifuge.
    10. Remove the supernatant in the collection tube, leaving 100 µL of solution in the tube. Mix the remaining sample by pipetting and transfer the sample to the new 1.5 mL centrifuge tubes marked OT (One touch 2 system).
      NOTE: When pipetting the supernatant, avoid touching the tube bottom along the side.
    11. Pipette 100 µL of nuclease-free water into each of the collection tubes, and transfer solution to the OT tube washed with repeated pipetting. Add 600 µL of nuclease-free water to the OT tube to make the total volume 1 mL, vortex for 30 s, and centrifuge at 15,500 x g for 8 min.
    12. Gently remove the supernatant in the OT tube with 100 µL remaining and use the tip to discard the oil layer thoroughly. Add 900 µL of nuclease-free water, vortex for 30 s, and centrifuge at 15,500 x g for 8 min.
    13. Remove the supernatant until 20 µL is left, add template resuspending solution to make the volume 100 µL, vortex for 30 s, and briefly centrifuge for 2 s.
      NOTE: The solution obtained in this step must proceed to the next step in less than 12 h.
    14. Run the clean program on the template amplification system before shutting down its power.
  3. Template enrichment
    1. Prepare the melt-off mix with 280 µL of tween-80 and 40 µL of 1 M NaOH.
    2. Wash the C1 beads. Vortex the C1 beads solution for 30 s. Transfer 100 µL of beads to a 1.5 mL centrifuge tube, insert the tube on a magnetic rack for 2 min and discard the supernatant.
    3. Transfer 1 mL of the C1 beads washing solution into the tube and vortex for 30 s. Centrifuge briefly (5 s), insert the tube into the magnetic rack for 2 min, and discard the supernatant. Pipette 130 µL of C1 bead resuspension solution into the tube, and mix the beads by repeated pipetting. Avoid creating bubbles.
    4. Load 100 µL of the diluted library, 130 µL of C1 beads, 300 µL x 3 template washing solution, and 300 µL of the melt-off solution to the eight-well strips, as shown in Figure 1.
    5. Install the eight-well strips on the enrichment module, load the pipetting tip, and set the 200 µL centrifuge tube in the collection position. Press on START to run the program; it takes about 35 min.
    6. The sample will automatically be collected in the 200 µL centrifuge tube; close the lid and centrifuge it at 15,500 x g for 5 min. Check the tube bottom to verify if any C1 beads remain.
    7. If C1 beads are remaining, repeatedly pipette the template solution 10x and insert the tube on the magnetic rack for 4 min. Transfer all the supernatant to a new 0.2 mL centrifuge tube and centrifuge at 15,500 x g for 5 min.
    8. If no visible C1 beads are remaining, discard the supernatant till 10 µL is left, add 200 µL of nuclease-free water, and mix by pipetting 10x. Centrifuge at 15,500 x g for 5 min.
    9. Discard the supernatant with 10 µL remaining, and add 90 µL of nuclease-free water to reach a total volume of 100 µL. Pipette up and down 10x to mix the solution, vortex for 5 s, and briefly centrifuge (5 s). The solution can be stored at 2-8 °C for less than 3 days.

5. Next-generation sequencing9,15

NOTE: All procedures in this section are performed on the DA8600 sequencing platform. Materials used in this section are available in the Sequencing Kit Set (Reagents/Solutions/Materials) of the Sequencing Reactions Universal Kit (Table of Materials).

  1. Check all reagents and materials required in a run-on sequencing platform.
    1. Sequencing reagent: Check for the availability of sequencing enzyme solution (6 µL), sequencing primers (20 µL), quality control template (5 µL), and dGTP/dCTP/dATP/dTTP (70 µL), stored between -30-10 °C.
    2. Sequencing solution: Check for the availability of sequencing solution II (100 mL), sequencing Solution III (50 mL), annealing buffer (1,015 µL), loading buffer (10 µL), foaming agent (2 µL), chlorine tablet (1 tablet), and Streptavidin beads (100 µL), stored at 4 °C.
    3. Materials: Check for the availability of 250 mL reagents tube (8), 250 reagents tube cap (8), sipper II (8), sipper (1), 2 L reagent bottle (1), and sequencing chip (1), stored at RT.
  2. Wash the chip before use.
    1. Set one chip steady on a working plate, inject 100 µL of nuclease-free water into the sample hole, remove the solution in the out portal, and repeat the procedure.
    2. Inject 100 µL of 0.1 M NaOH solution into the chip and incubate for 1 min at RT.
    3. Inject 100 µL of isopropanol into the sample hole, remove extra solution in the out portal, and repeat the procedure again.
    4. Cover the out portal with a filter paper, flow in the nitrogen to dry the remaining isopropanol in the chip's flow cell, and keep the ready-to-use chip at RT.
  3. Sequencer initiation
    1. Switch on the nitrogen valve and tune the pressure to 30 psi. Start the sequencer, press CLEAN on the main screen, and choose water or chloride to wash the machine accordingly.
      NOTE: Wash with water before every run, wash with chloride every week or the time the machine stands by with reagents over 48 h.
    2. Chloride wash: Choose one reagent bottle specified for chloride wash, wash the bottle twice with 18 MΩ water and fill the bottle with 1 L of 18 MΩ water. Put one chloride tablet into the bottle, dissolve the tablet for 10 min, add 1 mL of 1 M NaOH, and then reverse the bottle to mix the solution. Use the chloride solution within 3 h after preparation.
    3. Filter 100 mL of chloride solution with a 0.45 µm filter and collect with two tubes. Install the two chloride tubes into positions C1 and C2. Press CLEAN on the main screen, and equip a chip for chloride wash.
    4. Press on NEXT and check all steps on the screen to start the wash program; the program will end in 30 min. Start a wash with water after the chloride wash.
    5. Water wash: Mark two tubes specific for water with C1 and C2, and wash the tubes with 18 MΩ water twice. Add 100 mL of 18 MΩ water to each of the water wash tubes, and set them in C1 and C2 positions, respectively.
    6. Choose the CLEAN program, install the chip prepared for water wash, press NEXT, and then check all steps on the screen to start the wash program.
  4. Initialization
    1. Clean the wash bottle with wash solution II, mark it as W2, and wash it three times with 18 MΩ water.
    2. Clean the nitrogen tube with air-laid paper, insert it into the tube bottom, and tune the airflow to 0.5 L/min. Discharge the oxygen in the bottle and fill the bottle with 1,920 mL of 18 MΩ water. Add sequence solution II and 10 µL of 1 M NaOH to the bottle, close the cap, and reverse the bottle several times to mix the solution.
    3. Mark two new tubes as W1 and W3. Add 32 µL of 1 M NaOH to W1, add 40-50 mL of 1x sequence solution III to W3, and close the caps.
      NOTE: 1x sequence solution III must be in a 37 °C water bath for 30 min when first used. Sequence solution II must be protected from light and stored at RT. The wash bottle must be replaced with a new one after being used 20 times.
    4. Press INITIALIZE on the main screen, change the sipper on the W1, W2, and W3 positions, set the tubes to their position accordingly, and seal them tightly by rotation. Install a chip for initialization and check the state parameters of the machine.
    5. Press NEXT to start the initialization program; it takes 40 min in the first section.
      NOTE: The gloves must be changed before changing the new sipper to avoid contaminating the body of the sipper. Once used for water wash and initialization, the chips can be applied to initialization, but do not use the chips used for chloride-wash chips for initialization.
    6. Dissolve dGTP, dCTP, dATP, and dTTP on ice, and vortex to mix. Mark four new tubes as G, C, A, and T, and pipette 70 µL of the solution according to the tag of the tube.
  5. Prepare library for running.
    1. Place the quality control template, primers, and enzyme solution on ice.
    2. Prepare the DNA library when the initialization program hass about 20 min left. Vortex the quality control template for 30 s to mix, and briefly centrifuge for 2 s. Transfer 5 µL of the quality control template into the template solution, vortex for 5 s, and centrifuge the tube for 15,500 x g for 5 min. Remove the supernatant by carefully pipetting, avoid touching the pellet, and leave a 10 µL volume in the tube.
    3. Add 15 µL of annealing buffer into the tube; the total volume of the solution is 25 µL.
    4. Vortex the sequence primers when it fully dissolves on ice and centrifuge briefly for 2 s. Transfer 20 µL of the sequence primers into the tube from the former step, vortex for 5 s, shortly centrifuge for 2 s, and then store at RT before use.
  6. Loading the sample and sequencing
    1. Pipette 55 µL of the sample solution prepared in the previous step and inject it into the sample hole of the chip.
    2. Set the chip on the centrifuge; keep the notch towards the outside and the sample portal inside, balancing it with another used chip, and centrifuge for 10 min.
    3. Prepare the loading solution.
      1. Mix 0.5 mL of the annealing buffer and 0.5 mL of nuclease-free water in a 1.5 mL centrifuge tube. Mark it as 50% annealing buffer and use within 7 days.
      2. Mix 0.5 mL of isopropanol solution and 0.5 mL of annealing buffer. Mark it as 50% wash buffer and use within 24 h.
      3. Mix 6 µL of sequence enzyme and 60 µL of 50% annealing buffer. Mark it as enzyme reaction buffer, and place the solution on ice after preparation.
      4. Mix 49 µL of 50% annealing buffer and 1 µL of foaming agent, and mark it as foaming solution.
    4. Blow 100 µL of air into the foaming solution, repeatedly pipette the solution till the bubbles are in a dense foaming state, and keep the volume of foam around 250 µL.
    5. Place the chip on the bench after centrifuge, inject 100 µL of foam into the sample hole, and remove the extruded solution in the out portal. Set the chip back in the centrifuge, and centrifuge briefly for 30 s.
    6. Repeat steps 5.6.4-5.6.5.
    7. Inject 100 µL of 50% washing buffer twice, and remove the extruded solution in the out portal after every injection.
    8. Inject 100 µL of 50% annealing buffer three times, and remove the extruded solution in the out portal after every injection.
    9. Inject 65 µL of 50% enzyme reaction buffer, avoid bubbles, and remove the extruded solution in the out portal.
    10. Stabilize the loaded chip at RT for 5 min, and install the chip on the sequencer chip portal. Choose the plan programmed in step 6, check the information, and start the run; it takes about 1.5 h to finish.
    11. Perform the water wash program within 72 h after the run ends. Perform the chloride wash before water wash when the time exceeds 72 h. Shut down the sequencer, and close the valve of the nitrogen.

6. Plan an instructed sequencing run in the reporter server system16

NOTE: All procedures in this section are performed on Ion Proton Sequencer with the reporter server system.

  1. Sign in to the server system, select the Plan tab, and click on Plan Template Run. Choose the Whole Genome as run type, and select the appropriate template from the list of planned run templates.
  2. In the Plan tab, enter or make the following selections:
    1. Enter a new run plan name according to the batch of samples, select hg19 (Homo sapiens) from the Reference Library dropdown list, and select None from the Target Regions and Hotspot Regions dropdown lists.
    2. Enter the number of barcodes used in the sample set, select a barcode from the dropdown list for each sample, and enter a unique, descriptive name, which can be helpful to group and track the sample. Avoid the use of the default Sample 1 and so on.
    3. Select None in the Ion Reporter tab, click Next, and select DNA in the application and Whole Genome as the target technique.
    4. In the Kits tab, verify the selections, or make changes while it is appropriate for a run.
      1. Select Ion Plus Fragment Library Kit from the Library Kit Type dropdown list. Select Ion PI HI-Q OT2 200 kit in the Template Kit dropdown list, and choose OneTouch as the default. Select Ion PI HI-Q Sequencing 200 kit from the Sequencing Kit dropdown list.
      2. Enter 300 flows, select Ion PITM Chip from the Chip Type dropdown list, and select IonXpress from the Barcode Set dropdown list.
      3. Cancel the selection of Mark as Duplicates Reads and the selection of Enable Realignment.
    5. Choose the appropriate plugin in the Plugins tab to perform data analysis in step 7. Complete the selections in the projects step, click on Next, and click the Plan Run in the lower right corner to list the Planned Runs.
    6. In the Planned Runs tab, select the newly created run and check all the settings in the review window.

7. Data analysis

  1. Analyze the copy number variants (CNVs) using a bioinformatics workflow.
    NOTE: The CNVs were analyzed in bioinformatics workflow with the implementation of an algorithm based on a hidden Markov model (HMM)17; the model uses read coverage across the genome to predict the copy number or whole-number ploidy status (i.e., 0, 1, 2, 3, etc.). The overall bioinformatics pipeline was built in the plugin of a sequence server system, which is demonstrated in Figure 2. The bioinformatics analysis step takes an average of 4 h to complete.

Representative Results

As the sequences plan finishes after the running process in the machine, the sequence server system reports the summary with descriptive information of data generated, chip status, ISP loading rate, and library quality, as shown in Figure 2. In this results demonstration, 17.6 G data in the total base was obtained, and the overall loading rate of ISP was 88% in the total wells of the chip; the heat map showed that the sample was evenly loaded on the total area of the chip (Figure 2A). In the representative run, 99,761,079 total reads were obtained, in which 77% were usable; in all wells loaded with ISP, 100% had templates enriched, in which 78% were clonal. Out of all clonal templates, 97% were qualified as the final library (Figure 2B). The average length of the read was 117 bp, 176 bp, and 174 bp with mean, median, and mode, respectively (Figure 2C). Peak counts of T, C, and A in adapt of templates were ~76, which is over the qualified cut-off line of 50 (Figure 2D). In all addressable wells with live ISPs, 99.5% were qualified as the constructed library, and a 20% polyclonal and low-quality library was filtered out. 76.6% of ISPs were qualified for further analysis (Figure 2E).

The result of copy number variants from a single sample S19030109-3 is demonstrated in Figure 3; the black dash line is normalized as a euploidy segment across 22 autosomes and sex chromosomes, the red line is normalized as aneuploidy chromosome region representing a 182.16 Mb mosaic trisomy of p16.3-q35.2 on chromosome 4, and a 33.13 Mb monosomy segment of q11.1-q13.33 on chromosome 22.

Representative reports of 12 samples using WGA kits and 13 samples by the one-step method using independently developed WGA reagents are respectively shown in Table 4 and Table 5, which include summary information of barcode ID, sample name, unique reads count, aligned reads mean length, mean depth, percentage of GC content, and chromosome variants mark. The chromosome variants mark demonstrated sex chromosome, location and size of duplication, and deletion on chromosomes.

Figure 1
Figure 1: Diagram of sample loading position on 8-well strip. Each well with loading contents indicated respectively. U stands for un-enriched sample, B stands for beads, and W stands for wash solution; the empty wells are also noted in the figure. Please click here to view a larger version of this figure.

Figure 2
Figure 2: Running summary: data size, ISP loading and metrics of library quality. (A) The overall status, including total bases, key signal, and ISP loading rate with a heat map. (B) Total reads, usable reads rate, and summary of ISP information in each reaction step. (C) The histogram of reading length. (D) Consensus Key 1-Mer of TCA. (E) Addressable wells and IPS clonal status. Please click here to view a larger version of this figure.

Figure 3
Figure 3: Example of visualized copy number variants plot: S19030109-3. Copy number (CN) signals are visualized in a plot with blue and green intervals for chromosomes next to each other. The given example shows an increased observation of CN in chromosome 4 and a decreased observation of CN in chromosome 22, as the average CNV line noted in red falls offset from 2. Please click here to view a larger version of this figure.

No. of cycles Temperature Time
1 cycle 95 °C 2 min
12cycles 95 °C 15 s
15 °C 50 s
25 °C 40 s
35 °C 30 s
65 °C 40 s
75 °C 40 s
1 cycle 4 °C Hold

Table 1: Thermal cycle program for pre-amplification. Thermal reaction conditions such as temperature, time, and cycles are shown.

Step Temperature Time No. of cycles
1 95 °C 2 min 1
2 95 °C 15 s 14
65 °C 1 min
75 °C 1 min
3 4 °C hold 1

Table 2: Thermal cycle program for whole genome amplification with whole genome amplification kits. Thermal reaction conditions such as temperature, time, and cycles are shown.

Step Temperature (°C) Time No. of cycles
1 95 °C 2 min 30 s 1
2 95 °C 30 s 6
25°C 2 min
0.3 °C/s to 72 °C ——
72 °C 1 min 30 s
3 95 °C 30 s 20
62 °C 30 s
72 °C 1 min
4 72 °C 2 min 1
5 4 °C hold 1

Table 3: Thermal cycle program for whole genome amplification with the independently developed reagents. Thermal reaction conditions such as temperature, time, and cycles are shown.

Sample Name Unique Reads Count Aligned Reads Mean length Mean Depth CG% SD Mark
S19030109-1 913830 99.86 177.05 0.114 46.84 2.501 XY
S19030109-2 1277192 99.88 176.7 0.164 47.01 2.641 XX, +chr8
{p23.3->q24.3(139.13Mb)}
S19030109-3 992646 99.89 177.06 0.122 46.77 2.388 XX, +chr4{p16.3->q35.2(182.16Mb)},
-chr22{q11.1->q13.33(33.13Mb)}
S19030401-5 1657811 99.93 176.23 0.193 45.02 2.649 XY
S19030401-6 1738015 99.93 176.45 0.203 44.93 2.73 XY
S19030401-7 1444375 99.92 177.01 0.174 44.9 2.459 XX, +chr11{p15.5->q25(128.36Mb)},
-chr7{p22.3->q36.3(151.74Mb)}
S19030401-8 1792390 99.92 176.48 0.214 44.81 2.283 XY
S19030401-9 1802221 99.93 176.72 0.216 44.85 2.614 XX
S19030401-10 1932425 99.95 176.5 0.233 45.41 3.405 XX
S19030402-1 1916686 99.92 176.83 0.239 45.06 3.452 XY,+chr15
{q11.1->q21.1(23.93Mb)}
S19030402-2 1608840 99.94 176.92 0.191 44.71 2.65 XX,-chr22
{q11->q13.1(21.19Mb)}
S19030402-3 1505603 99.92 176.56 0.18 44.74 2.34 XY

Table 4: Example output of copy number variation using whole genome amplification kits in server system report. A typical output sheet includes parameters such as sample name, unique reads count, aligned reads, mean length, mean depth, CG percentage, the standard deviation of length, and for most, the mark of chromosome status with sex chromosome tagged with XY and concluded CNV detail. A detected CNV is marked with chromosome location and fragment size.

Sample Name Unique Reads Count Aligned Reads Mean Length Mean Depth GC% SD Mark
S21032201-8 1046608 99.93 178.69 0.055 40.49 2.532 XY
S21032201-9 1152585 99.95 178.17 0.051 40.93 2.437 XX
S21032201-10 1072667 99.94 178.31 0.046 40.69 2.687 XY,+chr21
{q11.2->q22.3(32.03Mb)}
S21032201-11 1067195 99.96 178.05 0.052 40.51 2.847 XX,-chr2
{p25.3->p11.2(80.34Mb)}
S21032203-1 1539227 99.93 177.96 0.064 40.84 2.109 XX
S21032203-2 1577847 99.96 178.11 0.044 40.52 2.508 XYY,+chr2
 {p25.3->q37.3(231.59Mb)}
S21032203-3 1240175 99.96 177.35 0.043 40.57 2.594 XY
S21032203-4 1216749 99.95 178.49 0.044 40.71 2.434 XX
S21032203-5 1191443 99.94 177.57 0.04 41.06 2.464 XX,-chr22
{q11.1->q13.33(33.13Mb)}
S21032203-6 1045673 99.9 177.86 0.039 41 2.418 XY
S21032211-1 962063 99.94 177.62 0.041 40.4 2.729 XX,+chr15
{q11.1->q13.3(12.66Mb)},
+chr2 {p25.3->p25.1(11.19Mb)}
S21032211-2 915407 99.95 178.15 0.034 40.48 2.747 XX
S21032211-3 911129 99.92 178.53 0.055 40.59 2.436 XY

Table 5: Example output of copy number variation by one-step method with the independently developed whole genome amplification reagents in server system report. A typical output sheet includes parameters such as sample name, unique reads count, aligned reads, mean length, mean depth, CG percentage, the standard deviation of length, and for most, the mark of chromosome status with sex chromosome tagged with XY and concluded CNV detail. A detected CNV is marked with chromosome location and fragment size.

Supplementary File 1: The recommended volume of each component when preparing a master mix of different batch sizes. Please click here to download this File.

Discussion

Chromosomal aneuploidy of embryos is the cause of a large proportion of pregnancy loss, whether conceived naturally or in vitro fertilization (IVF). In the clinical practice of IVF, it is proposed that screening the embryo aneuploidy and transferring the euploidy embryo could improve the outcome of IVF. Fluorescence in situ hybridization is the earliest technique adopted for sex selection and PGT-A; however, this technique requires more technical expertise from laboratory personnel and is relatively labor-intensive. Increasing studies of PGT-A using fluorescence in situ hybridization show no improvement in live birth rates17,18.

However, rapid advances in technologies have been made to assess the copy number analysis in pre-implantation genetic testing; different methods have their pros and cons. Newly developed comprehensive molecular techniques such as quantitative fluorescence PCR, single nucleotide polymorphism (SNP) array, array comparative genomic hybridization (aCGH), and next-generation sequencing showed promise in improving IVF outcomes7. Among these, NGS has high consistency with array-comparative genomic hybridization despite its scalability, higher throughput, easier automation, and more potential to reduce cost19,20,21.

In combination with WGA techniques, NGS analysis of embryo biopsy could provide more accurate sequence information, and also has a viable extension for more targets of single nucleotide level. With the increasing application of next-generation sequencing in detecting genetic abnormality, there is an urgent need to build standards for sample/data process both in the laboratory and clinical practice22,23,24.

In the path from separation to aneuploidy identification of the PGT-A process, the key steps include the separation, the selection of whole genome amplification method, the selection of next-generation sequencing platform, and the analysis of sequencing data. The whole genome amplification process is the most critical step in PGT-A, which determines the integrity and uniformity of sequencing data. Three whole genome amplification strategies were compared in a previous study, and it is proven that the picoPLEX quasi-random primer method performs almost as well as multiple displacement amplification (MDA) methods in terms of the integrity and uniformity of sequencing data25. Since clinical practice focuses on copy number variations (CNVs) at the resolution of ~10 Mbp rather than single nucleotide variation in PGT-A, the picoPLEX WGA kit and the independently developed WGA reagents were selected due to economic concerns. In the amplification stage, the latter requires only one step to complete the amplification of the whole genome, without the need for pre-amplification.

There are two main commercial platforms in the market currently being used for PGT: the MiSeq from Illumina26 and the Ion Proton from Thermo-Fisher Scientific27. Both Miseq and Proton can identify whole chromosome aneuploidy, but Miseq is only designed for identifying aneuploidy of the whole chromosome, while the Proton can also identify large deletions (dels) or duplications (dups), including clinically significant dels or dups down to a resolution of approximately 800 kb to 1 Mb28. The Proton platform has cost advantages and strong local technical support. For these reasons, the Proton platform was selected for later clinical practice.

The bioinformatics analysis of next-generation sequencing data is complicated and challenging for clinicians in clinical applications. With the increase of data in the public archive of human genetic variants and interpretations like Clinvar29, 1000 genome30, and Online Mendelian Inheritance in Man (OMIM)31, more CNV annotations software applications have been developed and are available for public and private use32,33. Here, a locally designed information system, Darui-LIMS, was applied to assist laboratory staff and clinicians to complete the CNV data analysis with one click in clinical practice of PGT-A34.

Our methods are designed specifically for PGT-A and have a good balance between resolution, accuracy, and cost. Standard procedures in genetic material processing and bioinformatics pipeline could produce consistent data for clinical analysis. With new advances in technologies based on the NGS system, additional chromosome structural abnormalities such as translocation can be tested and diagnosed for clinical amplification in the PGT cycle35,36. For these tests, more specialized methods need to be developed and applied. Even so, as a specification for guiding the clinical practice of PGT-A, these methods would be helpful for laboratory staff and clinicians in the laboratory practice of PGT-A on the DA8600 next-generation sequencing platform.

However, this method has certain limitations. In the protocol, the maximum number of samples that a magnetic rack can support is 16; of course, depending on the actual number of clinical samples, one can also choose a magnetic rack to support more samples at a time or increase the number of the magnetic rack to perform more sample operations. However, this may increase the risk of operational errors. Therefore, commercial kits based on semiconductor sequencing are recommended when working on batches of 32 samples or larger, such as Ion ReproSeq PGS Kits of Thermo-Fisher Scientific.

According to the Technical Evaluation Guidelines for Quality Control Technology of Preimplantation Chromosomal Aneuploidy Detection Reagents (High Throughput Sequencing) promulgated by the China National Institutes for Food and Drug Control, the requirement for the valid data volume of a single sample is not less than 1 M. There are 60-80 M reads per chip according to the Ion PI Product overview, and based on the experimental experience, the valid unique reads numbers are not less than 50% of the original data. After calculation, the effective data volume of each experimental sample is not less than 2 M. Therefore, to ensure the accuracy of the experimental results, we recommend a maximum capacity of 16 samples.

Açıklamalar

The authors have nothing to disclose.

Acknowledgements

We would like to thank Dr. Zhangyong Ming and Mr. Rongji Hou for their advice on LIMS expanded application. This study is supported by PLA Special Research Projects for Family Planning (17JS008, 20JSZ08), Fund of Guangxi Key Laboratory of Metabolic Diseases Research (No.20-065-76), and Guangzhou Citizen Health Science and Technology Research Project (201803010034).

Materials

0.45 μm Syringe Filter Unit Merkmillipore Millex-HV
1.5 mL DNA LoBind Tubes Eppendorf 30108051
15 mL tubes Greiner Bio-One 188261
2.0 mLDNA LoBind Tubes Eppendorf 30108078
50 mL tubes Greiner Bio-One 227261
5x Anstart Taq Buffer (Mg2+ Plus) FAPON
 Anstart Tap DNA Polymerase FAPON
AMPure XP reagent (magnetic beads for dna binding) Beckman A63881 https://www.beckman.com/reagents/genomic/cleanup-and-size-selection/pcr/a63881
Cell Lysis buffer Southern Medical University Cell lysis buffer containing 40 mM Tris (pH 8), 100 mM NaCl, 2 mM EDTA, 1 mM ethylene glycol tetraacetic acid (EGTA), 1% (v/v) Triton X-100, 5 mM sodium pyrophosphate, 2 mM β-glycerophosphate, 0.1% SDS
ClinVar NCBI https://www.ncbi.nlm.nih.gov/clinvar/
DNA elution buffer NEB T1016L
dNTP Vazyme P031-AA
DynaMag-2 Magnet Life Technologies 12321D
Ethyl alcohol Guangzhou Chemical Reagent Factory Thermo Fisher Scientific http://www.chemicalreagent.com/
Independently developed whole genome amplification reagents Southern Medical University The reagents consist of the following components:
1. Cell Lysis
2. Amplification Pre-mixed solution
    1) Primer WGA-P2 (10 μM)
    2) dNTP (10 mM)
    3) 5x Anstart Taq Buffer (Mg2+ Plus)
3. Amplification Enzyme
    1) Anstart Tap DNA Polymerase (5 U/μL)
Ion PI Hi-Q OT2 200 Kit Thermo Fisher Scientific A26434 Kit mentioned in step 4.2.8
Ion PI Hi-Q Sequencing 200 Kit   Thermo Fisher Scientific A26433
Ion Proton System Life Technologies 4476610
Ion Reporter Server System Life Technologies 4487118
isopropanol Guangzhou Chemical Reagent Factory http://www.chemicalreagent.com/
Library Preparation Kit Daan Gene Co., Ltd 114 https://www.daangene.com/pt/certificate.html
NaOH Sigma-Aldrich S5881-1KG
Nuclease-Free Water Life Technologies AM9932
Oligo WGA-P2 Sangon Biotech 5'-ATGGTAGTCCGACTCGAGNNNN
NNNNATGTGG-3'
OneTouch 2 System Life Technologies 4474779  Template amplification and enrichment system
PCR tubes Axygen PCR-02D-C
PicoPLEX WGA Kit Takara Bio USA R300671
Pipette tips Quality Scientific Products https://www.qsptips.com/products/standard_pipette_tips.aspx
Portable Mini Centrifuge LX-300 Qilinbeier E0122
Qubit 3.0 Fluorometer Life Technologies Q33216 Fluorometer
Qubit Assay Tubes Life Technologies Q32856
Qubit dsDNA HS Assay Kit Life Technologies Q32851
Sequencer server system Thermo Fisher Scientific Torrent Suite Software
Sequencing Reactions Universal Kit Daan Gene Co., Ltd 113 https://www.daangene.com/pt/certificate.html
This kit contains the following components:
1. Template Preparation Kit Set

1.1 Template Preparation Kit:
Emulsion PCR buffer
Emulsion PCR enzyme mix
Template carrier solution

1.2 Template Preparation solutions:
Template preparation reaction oil I
emulsifier breaking solution II
Template Preparation Reaction Oil II
Nuclease-free water
Tween solution
Demulsification solution I
Template washing solution
C1 bead washing solution
C1 bead resuspension solution
Template resuspension solution

1.3 Template Preparation Materials:
Reagent tube I
connector
Collection tube
Reagent tube pipette I
Amplification plate
8 wells strip
Dedicated tips
Template preparation washing adapter
Template preparation filter

2. Sequencing Kit Set

2.1 Sequencing Kit:
dGTP
dCTP
dATP
dTTP
Sequencing enzyme solution
Sequencing primers
Quality control templates

2.2  Sequencing Solutions:
Sequencing solution II
Sequencing solution IIII
Annealing buffer
Loading buffer
Foaming agent
Chlorine tablets
C1 bead

2.3 Sequencing Materials:
Reagent Tube II
Reagent tube cap
Reagent tube sipper  II
Reagent bottle sipper
Reagent bottles

3. Chip
Sodium hydroxide solution Sigma 72068-100ML
Thermal Cycler Life Technologies 4375786
DOWNLOAD MATERIALS LIST

Referanslar

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Etiketler

Pre-implantation Genetic TestingAneuploidySemiconductorNext-generation SequencingWhole Genome AmplificationDNA PurificationMagnetic BeadsEthanol WashEmulsifier Breaking SolutionTemplate Preparation

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Xu, C., Wei, R., Lin, H., Deng, L., Wang, L., Li, D., Den, H., Qin, W., Wen, P., Liu, Y., Wu, Y., Ma, Q., Duan, J. Pre-Implantation Genetic Testing for Aneuploidy on a Semiconductor Based Next-Generation Sequencing Platform. J. Vis. Exp. (186), e63493, doi:10.3791/63493 (2022).
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