Detection of candidate genes affecting milk production traits in sheep using whole‐genome sequencing analysis

AbstractSummaryWhole-genome sequencing (WGS) is a cornerstone of precision medicine, but portable and reproducible open-source workflows for WGS analyses of germline and somatic variants are lacking. We present Sarek, a modular, comprehensive, and easy-to-install workflow, combining a range of software for the identification and annotation of single-nucleotide variants (SNVs), insertion and deletion variants (indels), structural variants, tumor sample heterogeneity, and karyotyping from germline or paired tumor/normal samples. Sarek is implemented in a bioinformatics workflow language (Nextflow) with Docker and Singularity compatible containers, ensuring easy deployment and full reproducibility at any Linux based compute cluster or cloud computing environment. Sarek supports the human reference genomes GRCh37 and GRCh38, and can readily be used both as a core production workflow at sequencing facilities and as a powerful stand-alone tool for individual research groups.AvailabilitySource code and instructions for local installation are available at GitHub (https://github.com/SciLifeLab/Sarek) under the MIT open-source license, and we invite the research community to contribute additional functionality as a collaborative open-source development project.

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Whole-genome sequencing analysis of Y chromosome microdeletion: a case report

Journal of International Medical Research ◽

10.1177/0300060520976494 ◽

2020 ◽

Vol 48 (12) ◽

pp. 030006052097649

Author(s):

Zhixiang Gao ◽

Feng Yuan ◽

Qiaoqiao Li ◽

Renlan Xia ◽

Kai Fu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Y Chromosome ◽

Genome Sequencing ◽

Sperm Quality ◽

Sperm Count ◽

Therapeutic Targets ◽

Camp Signaling ◽

Whole Genome ◽

Sequencing Analysis ◽

Y Chromosome Microdeletion

The mechanisms by which Y chromosome microdeletions cause infertility have been well described; however, the therapeutic targets remain a challenge. Here, we used whole-genome sequencing to explore the mechanism of Y chromosome deletion and potential therapeutic targets in a patient with infertility. There were no abnormalities in the patient’s medical history. Routine semen analysis showed immotile sperm and only two motile spermatozoa were occasionally see after centrifugation, indicating that the direct cause of infertility was an abnormal sperm count and motility. A Y chromosome microdeletion test revealed partial deletion of the AZFc region, including AZFc1, AZFc2, AZFc3, and AZFc4. Whole-genome sequencing showed that the patient had seven harmful mutations, with only one significant epigenetic mutation, SH3KBP1. Gene Ontology analysis of these meaningful mutations indicated involvement of cAMP signaling pathways. The patient’s wife became pregnant following in vitro fertilization, and no significant abnormalities were found during prenatal examination. This case suggests that Y chromosome microdeletion and gene mutation may affect the cAMP signaling pathway, leading to reduced sperm quality and male infertility.

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484 Whole Genome Sequencing Analysis of Gastroparesis

The American Journal of Gastroenterology ◽

10.14309/01.ajg.0000591468.58949.41 ◽

2019 ◽

Vol 114 (1) ◽

pp. S280-S281

Author(s):

Sandra P. Smieszek ◽

Jesse L. Carlin ◽

Gunther Birznieks ◽

Mihael H. Polymeropoulos

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Sequencing Analysis

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