Evaluation of targeted exome sequencing for 28 protein-based blood group systems, including the homologous gene systems, for blood group genotyping

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Abstract

Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS.

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Statistical challenges associated with detecting copy number variations with next-generation sequencing.

Yudi Pawitan, Agus Salim, Kee Seng Chia … (2012)

Analysing next-generation sequencing (NGS) data for copy number variations (CNVs) detection is a relatively new and challenging field, with no accepted standard protocols or quality control measures so far. There are by now several algorithms developed for each of the four broad methods for CNV detection using NGS, namely the depth of coverage (DOC), read-pair, split-read and assembly-based methods. However, because of the complexity of the genome and the short read lengths from NGS technology, there are still many challenges associated with the analysis of NGS data for CNVs, no matter which method or algorithm is used. In this review, we describe and discuss areas of potential biases in CNV detection for each of the four methods. In particular, we focus on issues pertaining to (i) mappability, (ii) GC-content bias, (iii) quality control measures of reads and (iv) difficulty in identifying duplications. To gain insights to some of the issues discussed, we also download real data from the 1000 Genomes Project and analyse its DOC data. We show examples of how reads in repeated regions can affect CNV detection, demonstrate current GC-correction algorithms, investigate sensitivity of DOC algorithm before and after quality control of reads and discuss reasons for which duplications are harder to detect than deletions.

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Human Blood Groups

Geoff Daniels (2013)

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SMIM1 underlies the Vel blood group and influences red blood cell traits.

Ana Cvejic, Lonneke Haer-Wigman, Jonathan C Stephens … (2013)

The blood group Vel was discovered 60 years ago, but the underlying gene is unknown. Individuals negative for the Vel antigen are rare and are required for the safe transfusion of patients with antibodies to Vel. To identify the responsible gene, we sequenced the exomes of five individuals negative for the Vel antigen and found that four were homozygous and one was heterozygous for a low-frequency 17-nucleotide frameshift deletion in the gene encoding the 78-amino-acid transmembrane protein SMIM1. A follow-up study showing that 59 of 64 Vel-negative individuals were homozygous for the same deletion and expression of the Vel antigen on SMIM1-transfected cells confirm SMIM1 as the gene underlying the Vel blood group. An expression quantitative trait locus (eQTL), the common SNP rs1175550 contributes to variable expression of the Vel antigen (P = 0.003) and influences the mean hemoglobin concentration of red blood cells (RBCs; P = 8.6 × 10(-15)). In vivo, zebrafish with smim1 knockdown showed a mild reduction in the number of RBCs, identifying SMIM1 as a new regulator of RBC formation. Our findings are of immediate relevance, as the homozygous presence of the deletion allows the unequivocal identification of Vel-negative blood donors.

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Author and article information

Journal

Title: Transfusion

Abbreviated Title: EDITORIAL

Publisher: Wiley

ISSN: 00411132

Publication date Created: April 2017

Publication date (Print): April 2017

Publication date (Electronic): March 24 2017

Volume: 57

Issue: 4

Pages: 1078-1088

Affiliations

[1 ]Research and Development

[2 ]Red Cell Reference Laboratory; Australian Red Cross Blood Service; Brisbane Queensland Australia

Article

DOI: 10.1111/trf.14054

PubMed ID: 28338218

SO-VID: d5e2908e-f6aa-4414-a57b-e4d886dae635

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http://doi.wiley.com/10.1002/tdm_license_1

http://onlinelibrary.wiley.com/termsAndConditions

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Evaluation of targeted exome sequencing for 28 protein-based blood group systems, including the homologous gene systems, for blood group genotyping : SEQUENCING FOR BLOOD GROUP GENOTYPING

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Most cited references 16

Statistical challenges associated with detecting copy number variations with next-generation sequencing.

Human Blood Groups

SMIM1 underlies the Vel blood group and influences red blood cell traits.

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