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RH genotyping by nonspecific quantitative next‐generation sequencing
Author(s) -
Stef Marianne,
Fennell Katie,
Apraiz Izaskun,
Arteta David,
González Cecilia,
Nogués Nuria,
OchoaGaray Gorka
Publication year - 2020
Publication title -
transfusion
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.045
H-Index - 132
eISSN - 1537-2995
pISSN - 0041-1132
DOI - 10.1111/trf.16034
Subject(s) - zygosity , genotyping , genetics , biology , genotype , dna sequencing , structural variation , computational biology , gene , genome
Abstract Background Conventional sequencing uses gene‐specific primers to determine the location of RH variants and permits a qualitative assessment of zygosity. Whole‐genome and whole‐exome sequencing determine the genetic location of variants and enable a quantitative assessment of zygosity. Nonspecific sequencing uses RH ‐consensus primers to detect variants and sequencing‐read ratios to quantify their copy number. Study Design and Methods Two hundred seventy eight samples with diverse genotypes were analyzed by next‐generation sequencing with RH ‐ consensus primers. Custom‐developed data analysis software was used to detect individual variants and infer the RH genotype. The method was evaluated for its quantitative nature, its ability to discriminate similar genotypes, its accuracy to detect variants, and its accuracy to assign them to RHD or RHCE . Results As a measure of balanced amplification of RHD and RHCE sequences, observed ratio medians deviate from expected ratios by 3% or less of the ratio range. As a measure of discriminatory power, contiguous RHCE / [RHD + RHCE] ratio averages are separated by 4 or more standard deviations of the mean. Variants are detected with a sensitivity and specificity greater than 99%, and variants at consensus positions are correctly assigned to RHD vs RHCE with a sensitivity greater than 72% and a specificity greater than 99%. The method is successful in the identification of genotypes with large conversion events and in the detection of copy number variation. Conclusion Nonspecific sequencing of homologous gene sets combines detection and quantification of genetic variation in a single assay. Evidence is provided for the quantitative nature of the method, its sensitivity and specificity, and its ability to identify complex RH genotypes.