Phosphorus Research: A Comprehensive Genetic Assessment of Male and Female Infertility Using NGS
Last week, Phosphorus attended the American Society of Reproductive Medicine Scientific Congress & Expo in San Antonio, Texas. The ASRM Congress & Expo is a yearly forum where professionals gather to discuss developments in the field of reproductive medicine and share scientific findings. This year, Phosphorus was proud to present its scientific poster, entitled “A Comprehensive Genetic Assessment of Male and Female Infertility Using Next-Generation Sequencing.” The poster summarized Phosphorus’ attempt to develop a single NGS assay to replace a variety of other assays used to genetically assess infertility. Phosphorus’ study was undertaken to explore new ways to simplify the ordering process for healthcare providers, reduce turnaround time, and lower the overall cost of testing while increasing access to care.
Genetic assessment of male and female infertility typically involves several assays performed independently, including chromosome analysis for sex chromosome aneuploidy; PCR-based methods for Y chromosome microdeletions and CFTR poly-T tract analysis; and sequencing of genes associated with infertility. Our objective was to develop a comprehensive next-generation sequencing (NGS) panel incorporating these individual assays.
We designed a sequencing capture that included targeted regions of the X and Y chromosomes and genes associated with infertility, and developed a custom bioinformatics pipeline to call sex chromosome aneuploidies, Y chromosome microdeletions, CFTR poly-T tract variants, and identified sequencing variants.
Materials and Methods:
Targeted sequencing (NimbleGen/Illumina) was performed for distinct regions of the X and Y chromosomes, including the AZFa, AZFb, and AZFc regions, as well as exons, promoters, 5’-UTRs, 3’-UTRs, and selected introns of genes associated with infertility. Reads were aligned to hg19 (reference genome) and variants were called using DRAGEN and GATK algorithms. Sex chromosome aneuploidies and Y chromosome microdeletions were called using a previously described read-depth based algorithm. The assay was validated using samples from the 1000 Genomes Project and samples harboring known pathogenic variants.
Our results [included in poster, below] demonstrate that a single NGS assay may replace a variety of other assays as a genetic assessment of infertility. A comprehensive panel can simplify the ordering process for healthcare providers, reduce turnaround time, and lower the overall cost of testing while increasing access to care.
View the poster below:
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