Veriseq pgs kit

Manufactured by Illumina

Sourced in United States

The VeriSeq PGS Kit is a laboratory equipment product offered by Illumina. It is designed for preimplantation genetic screening (PGS) applications. The kit provides the necessary reagents and consumables for genetic analysis of embryonic samples.

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Lab products found in correlation

Miseq system, by Illumina (3 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Qubit 3.0 fluorimeter, by Thermo Fisher Scientific (2 mentions) Bluefuse multi software, by Illumina (2 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (2 mentions) Sureplex dna amplification kit, by Illumina (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Mastercycler nexus, by Eppendorf (1 mentions) Bluefuse multi, by Illumina (1 mentions) Sureplex kit, by Illumina (1 mentions) Sureplex dna amplification system, by Illumina (1 mentions) Miseqtm system, by Illumina (1 mentions)

9 protocols using veriseq pgs kit

NGS-based Aneuploidy Screening in IVF

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Since Karyomapping has not been fully validated for the purpose of aneuploidy screening, embryos considered to be unaffected that did not show numerical chromosomal abnormalities by Karyomapping were analyzed by NGS. Aliquots of the same whole-genome amplified trophectoderm samples were used for NGS-based technology by means of VeriSeq PGS Kit (Illumina, San Diego, CA, USA) on Illumina MiSeq TM System according to the manufacturer instructions and were analyzed by the BlueFuse Multi software (Illumina).
The VeriSeq PGS Kit uses an engineered transposome for the preparation of sequencing-ready libraries to tagment the input DNA. Subsequently, a limited-cycle PCR uses the adapter sequences to amplify the insert DNA and to add index sequences to both ends of the DNA. Prepared VeriSeq PGS libraries are pooled and run on the MiSeq system, where secondary analysis of the data is performed, demultiplexing and aligning the reads to the reference genome. Data obtained are imported into BlueFuse Multi Analysis software, which process and display the data to provide genomic profiles of each sample in a run. Whole chromosome aneuploidy is called automatically. The effective resolution of the assay is 20 Mb. The number of reads after filtering, sample overall noise score and average quality alignment scores were assessed according to the VeriSeq quality control parameters.

Sabria-Back J., Monteagudo-Sánchez A., Sánchez-Delgado M., Ferguson-Smith A.C., Gómez O., Pertierra Cartada A., Tenorio J., Nevado J., Lapunzina P., Pereda Aguirre A., Giménez Sevilla C., Toro Toro E., Perez de Nanclares G, & Monk D. (2022). Preimplantation genetic testing for a chr14q32 microdeletion in a family with Kagami-Ogata syndrome and Temple syndrome. Journal of medical genetics, 59(3).

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Comprehensive Chromosome Aneuploidy Screening

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DNA from all samples was amplified using SurePlex kit (BlueGnome) according to the manufactures instructions and quantified by Qubit3.0 Fluorimeter (Thermo Fisher Scientific). Amplified DNA was assessed for whole and segmental chromosome aneuploidy screening with a previously validated VeriSeq™ PGS kit on the MiSeq system (Illumina) in the CReATe Fertility Centre Genetics Laboratory [26 ].

Kuznyetsov V., Madjunkova S., Antes R., Abramov R., Motamedi G., Ibarrientos Z, & Librach C. (2018). Evaluation of a novel non-invasive preimplantation genetic screening approach. PLoS ONE, 13(5), e0197262.

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Comprehensive Embryonic CNV Profiling

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A genomic library was established using the tail tips of the parental B6D2F1 mice. WGA was performed using the SurePlex DNA Amplification kit (Illumina). The next-generation sequencing algorithm was used to determine the CNV of both the control and experimental embryos. CNV analysis was performed using VeriSeq PGS Kit (Illumina) and MiSeq Reagent Kit v3 - PGS (Illumina). The total CNV for all 20 chromosomes was plotted to visualize the embryo ploidy. For control embryos, the whole blastocyst was used. For experimental embryos, either the entire embryo or a biopsy of 4–8 trophectoderm cells was used. WGA was performed at the Center for Reproductive Medicine Preimplantation Genetic Testing Laboratory of Weill Cornell Medicine. Weill Cornell Medicine’s Applied Bioinformatics Core Laboratory Facility performed all bioinformatic analyses and sequencing.

Lee Y., Trout A., Marti-Gutierrez N., Kang S., Xie P., Mikhalchenko A., Kim B., Choi J., So S., Han J., Xu J., Koski A., Ma H., Yoon J.D., Van Dyken C., Darby H., Liang D., Li Y., Tippner-Hedges R., Xu F., Amato P., Palermo G.D., Mitalipov S, & Kang E. (2022). Haploidy in somatic cells is induced by mature oocytes in mice. Communications Biology, 5, 95.

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Comprehensive Chromosomal Analysis of POCs

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Conventional G‐banding analysis was carried out by Nihon Gene Research Laboratories Inc. For NGS‐based chromosomal copy number analysis, chorionic villi were collected from POC. To prevent maternal cell contamination, only distinct chorionic villus was collected under the stereomicroscope and maternal tissue (eg, endometrium or peripheral blood) was removed as much as possible. Genomic DNA was isolated using the QIAamp DNA Mini Kit (Qiagen GmbH) according to the manufacturer's instructions. Library construction was performed using the VeriSeq PGS kit (Illumina), and the MiSeq system (Illumina) was used for DNA sequencing following the manufacturer's protocol with minor modification. G‐banding and NGS analysis were carried out in different laboratories which were registered clinical laboratory by Japan Registered Clinical Laboratories Association. Each laboratory performed quality control internally and externally; however, G‐banding and NGS analysis were different not only quality control method but also detection principle and obtained results. Thus, we had to comprehensively consider the data quality, specificity, possibility of contamination, and so on, when obtained inconsistent test results.

Tamura Y., Santo M., Araki Y., Matsubayashi H., Takaya Y., Kitaya K., Doshida M., Yamaguchi K., Mizuta S., Takahashi C., Kim N., Okuno K., Takeuchi T, & Ishikawa T. (2020). Chromosomal copy number analysis of products of conception by conventional karyotyping and next‐generation sequencing. Reproductive Medicine and Biology, 20(1), 71-75.

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NGS Analysis of TE Biopsy Samples

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Tubing and NGS analysis of cell specimens obtained through TE biopsy were performed according to the method described by Takeuchi et al.²¹ Briefly, as a preliminary preparation, we entered the sample number in the dish (Falcon 351007) to wash the sample cells and a 0.2‐ml tube (Eppendorf polymerase chain reaction [PCR] tubes 0.2 ml) to store the sample. The Pasteur pipette tip was lightly washed with polyvinyl pyrrolidone (Origio) to prevent cell stickiness. After washing the sample three times with phosphate‐buffered solution, it was moved to the bottom of the 0.2‐ml tube, and the tube lid was closed. After centrifugation, the samples were stored at −20°C. The actual NGS procedures were as follows: First, the whole sample was subjected to whole‐genome amplification using a Veriseq PGS kit (Illumina) and a thermal cycler (Mastercycler Nexus, Eppendorf); the obtained sample was quantified and diluted to 0.2 ng/μl, and the diluted sample was amplified using a docosahexaenoic acid tag and PCR. After amplification, cleanup and normalization were performed, as well as load library formation, pooling and loading. The next day, the obtained data were subjected to chart analysis using BlueFuse Multi Software (Illumina).

Mizobe Y., Kuwatsuru Y., Kuroki Y., Fukumoto Y., Tokudome M., Moewaki H., Watanabe M., Iwakawa T, & Takeuchi K. (2022). The effects of differences in trophectoderm biopsy techniques and the number of cells collected for biopsy on next‐generation sequencing results. Reproductive Medicine and Biology, 21(1), e12463.

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Whole Genome NGS for Embryo Ploidy

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Whole genome copy number variation (CNV) analysis was performed by whole genome low pass (0.1×) NGS using the VeriSeq® PGS Kit (Illumina, CA). Briefly, after WGA, according to manufacturer’s instructions, gDNA was tagmented and amplified. The amplified gDNA was indexed, purified using AMPure XP beads (1:1 ratio), and normalized using magnetic beads. The normalized libraries were pooled, denatured, and sequenced using a MiSeq (single-end, 1 × 36 bp). BlueFuse Multi (Illumina, CA) was used for chromosome CNV analysis and data visualization. The optimal metrics for standard clinical analysis of embryo ploidy are 500,000 reads passing filter and a sample noise score (derivative log ratio - DLR) of <0.2; 250,000 reads and DLR < 0.4 is clinically acceptable.

Fuchs Weizman N., Wyse B.A., Antes R., Ibarrientos Z., Sangaralingam M., Motamedi G., Kuznyetsov V., Madjunkova S, & Librach C.L. (2019). Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy. Scientific Reports, 9, 2853.

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Comprehensive Aneuploidy Screening of Embryos

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DNA from all samples was amplified using SurePlex kit (Illumina), according to the manufacturer's instructions, and quantified by Qubit3.0 Fluorimeter (Thermo Fisher Scientific). Amplified DNA was assessed for whole and segmental chromosome aneuploidy screening with a previously validated VeriSeq PGS kit on the MiSeq system (Illumina) in the CReATe Fertility Centre Genetics laboratory (34) . Embryos with available PGT-A results were classified as euploid, aneuploid or mosaic (10 Mb resolution; 30%-70% mosaicism).

Dviri M., Madjunkova S., Koziarz A., Antes R., Abramov R., Mashiach J., Moskovtsev S., Kuznyetsova I, & Librach C. (2020). Is there a correlation between paternal age and aneuploidy rate? An analysis of 3,118 embryos derived from young egg donors. Fertility and sterility, 114(2).

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Whole Genome Amplification and NGS Profiling

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Sample cell preparation, cell lysing procedures, DNA extraction, and whole genome amplification (WGA) were performed using the SurePlex DNA Amplification System (Illumina, San Diego, CA, USA), according to the manufacturer’s recommended conditions. The DNA concentration of the product after amplification was measured using a Qubit 3.0 Fluorometer (ThermoFisher Scientific) with the Qubit dsDNA HS Assay kit (ThermoFisher Scientific).
Following WGA, the samples were treated using a VeriSeq PGS Kit (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions. NGS was performed using a MiSeq testing device (Illumina, San Diego, CA, USA). The obtained data were analyzed using Bluefuse Multi software to obtain the karyotype information of the sample.

Shitara A., Takahashi K., Goto M., Takahashi H., Iwasawa T., Onodera Y., Makino K., Miura H., Shirasawa H., Sato W., Kumazawa Y, & Terada Y. (2021). Cell-free DNA in spent culture medium effectively reflects the chromosomal status of embryos following culturing beyond implantation compared to trophectoderm biopsy. PLoS ONE, 16(2), e0246438.

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Preimplantation Genetic Screening via NGS

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Preimplantation genetic screening was carried out using trophectoderm biopsy on day 5 or day 6 and next-generation sequencing. Amplified samples for next-generation sequencing were processed with VeriSeq PGS kit (Illumina). Blastocysts were vitrified after biopsy and warmed on the same day as embryo transfer.

Kellam L., Pastorelli L.M., Bastida A.M., Senkbeil A., Montgomery S., Fishel S, & Campbell A. (2017). Perivitelline threads in cleavage-stage human embryos: observations using time-lapse imaging. Reproductive biomedicine online, 35(6).

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