Volume 18, Issue 5 (May 2020)                   IJRM 2020, 18(5): 375-384 | Back to browse issues page

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Askari M, Kordi Tamandani D M, almadani N, Totonchi M. Strategies for whole-exome sequencing analysis in a case series study of familial male infertility. IJRM 2020; 18 (5) :375-384
URL: http://ijrm.ir/article-1-1302-en.html
Strategies for whole-exome sequencing analysis in a case series study of familial male infertility
Masomeh Askari1 , Dor Mohammad Kordi Tamandani * 2, Navid Almadani3 , Mehdi Totonchi4
1- Department of Biology, Sistan and Baluchestan University, Zahedan, Iran.
2- Department of Biology, Sistan and Baluchestan University, Zahedan, Iran. , dor_kordi@science.usb.ac.ir
3- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
4- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
Abstract:   (2364 Views)
Background: Infertility is one of the common health issues around the world. The prevalence of male factor infertility among infertile couples is approximately 30%-35%, of which genetic factors account for 15%. The family-based whole-exome sequencing (WES) approach can accurately detect novel variants. However, selecting an appropriate sample for data generation using WES has proven to be challenging in familial male infertility studies. The aim of this study was to identify types of pathogenic male infertility in cases of familial asthenozoospermia.
Case: Two families with multiple cases were recruited for the purpose of WES. The study population included two affected cases in pedigree I and three affected cases in pedigree II. Two different variant callers (SAMtools and GATK) with a single-sample calling strategy (SSCS) and a multiple-sample calling strategy (MSCS), were applied to identify variant sites.
Conclusion: In this study, we represented the results for variant prioritization of WES data without sequencing fertile siblings in the same pedigree by applying two different pipelines (homozygosity and linkage-based strategy). Using the aforementioned strategies, we prioritized annotated variants and generated a logical shortlist of private variants for each pedigree.
 
Keywords: Male infertility, Whole-exome sequencing, GATK, SAMtools.
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Type of Study: Original Article | Subject: Reproductive Genetics
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