scholarly journals Homozygosity Mapping using Whole-Exome Sequencing: A Valuable Approach for Pathogenic Variant Identification in Genetic Diseases

Author(s):  
Jorge Oliveira ◽  
Rute Pereira ◽  
Rosário Santos ◽  
Mário Sousa
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alana R. Rodney ◽  
Reuben M. Buckley ◽  
Robert S. Fulton ◽  
Catrina Fronick ◽  
Todd Richmond ◽  
...  

AbstractOver 94 million domestic cats are susceptible to cancers and other common and rare diseases. Whole exome sequencing (WES) is a proven strategy to study these disease-causing variants. Presented is a 35.7 Mb exome capture design based on the annotated Felis_catus_9.0 genome assembly, covering 201,683 regions of the cat genome. Whole exome sequencing was conducted on 41 cats with known and unknown genetic diseases and traits, of which ten cats had matching whole genome sequence (WGS) data available, used to validate WES performance. At 80 × mean exome depth of coverage, 96.4% of on-target base coverage had a sequencing depth > 20-fold, while over 98% of single nucleotide variants (SNVs) identified by WGS were also identified by WES. Platform-specific SNVs were restricted to sex chromosomes and a small number of olfactory receptor genes. Within the 41 cats, we identified 31 previously known causal variants and discovered new gene candidate variants, including novel missense variance for polycystic kidney disease and atrichia in the Peterbald cat. These results show the utility of WES to identify novel gene candidate alleles for diseases and traits for the first time in a feline model.


2021 ◽  
Vol 22 (19) ◽  
pp. 10400
Author(s):  
H. Busra Cagirici ◽  
Bala Ani Akpinar ◽  
Taner Z. Sen ◽  
Hikmet Budak

The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.


2016 ◽  
Vol 98 ◽  
Author(s):  
LIOR COHEN ◽  
SHAY TZUR ◽  
NITZA GOLDENBERG-COHEN ◽  
CONCETTA BORMANS ◽  
DORON M. BEHAR ◽  
...  

SummaryInherited optic neuropathies are a heterogeneous group of disorders characterized by mild to severe visual loss, colour vision deficit, central or paracentral visual field defects and optic disc pallor. Optic atrophies can be classified into isolated or non-syndromic and syndromic forms. While multiple modes of inheritance have been reported, autosomal dominant optic atrophy and mitochondrial inherited Leber's hereditary optic neuropathy are the most common forms. Optic atrophy type 1, caused by mutations in theOPA1gene is believed to be the most common hereditary optic neuropathy, and most patients inherit a mutation from an affected parent. In this study we used whole-exome sequencing to investigate the genetic aetiology in a patient affected with isolated optic atrophy. Since the proband was the only affected individual in his extended family, and was a product of consanguineous marriage, homozygosity mapping followed by whole-exome sequencing were pursued. Exome results identified a novelde novo OPA1mutation in the proband. We conclude, that thoughde novo OPA1mutations are uncommon, testing of common optic atrophy-associated genes such as mitochondrial mutations andOPA1gene sequencing should be performed first in single individuals presenting with optic neuropathy, even when dominant inheritance is not apparent.


2018 ◽  
Vol 94 (5) ◽  
pp. 419-428 ◽  
Author(s):  
X. Lu ◽  
Q. Wang ◽  
H. Gu ◽  
X. Zhang ◽  
Y. Qi ◽  
...  

2019 ◽  
Vol 497 ◽  
pp. 88-94
Author(s):  
Tsz-ki Ling ◽  
Chun-yiu Law ◽  
Kin-wing Yan ◽  
Nai-chung Fong ◽  
Ka-chung Wong ◽  
...  

2020 ◽  
Vol 42 (8) ◽  
pp. 587-593
Author(s):  
Jamil A. Hashmi ◽  
Fatima Fadhli ◽  
Ahmed Almatrafi ◽  
Sibtain Afzal ◽  
Khushnooda Ramzan ◽  
...  

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