scholarly journals Detection of Clinically Relevant Genetic Variants in Chinese Patients With Nanophthalmos by Trio-Based Whole-Genome Sequencing Study

2019 ◽  
Vol 60 (8) ◽  
pp. 2904 ◽  
Author(s):  
Congcong Guo ◽  
Zhenni Zhao ◽  
Denghui Chen ◽  
Shuxiang He ◽  
Nannan Sun ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Chinese Patients ◽  
Whole Genome

scholarly journals Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

2013 ◽  
Vol 93 (2) ◽  
pp. 249-263 ◽  
Author(s):  
Yong-hui Jiang ◽  
Ryan K.C. Yuen ◽  
Xin Jin ◽  
Mingbang Wang ◽  
Nong Chen ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Whole Genome

Whole-genome sequencing of athletes: the effect of nonsense mutations on functional variables

2021 ◽  
pp. 19-29
Author(s):  
Е.А. Булыгина ◽  
О.В. Борисов ◽  
Е.В. Валеева ◽  
Е.А. Семенова ◽  
А.К. Ларин ◽  
...  
Keyword(s):  
Lower Extremity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Mutant Allele ◽  
Peak Power ◽  
Protein Translation ◽  
Whole Genome ◽  
Homozygous State ◽  
Nonsense Mutations

Применение технологии полногеномного секвенирования предоставляет обширные возможности для обнаружения новых генетических маркеров, определяющих результативность спортсмена. Целью исследования является определение особенностей геномного профиля спортсменов высокого класса и выявление генетических вариантов, ассоциированных с некоторыми функциональными показателями, влияющими на спортивную успешность. Впервые проведено секвенирование геномов 20 профессиональных борцов татарской национальности. Найденные генетические варианты валидированы с использованием ДНК-микрочипов и/или импутации. Из всего спектра полиморфных вариантов отобраны мутации в гомозиготном состоянии, имеющие аннотацию «stop gain» (нонсенс-мутации) и показавшие ассоциацию со следующими фенотипами: мышечная масса, пиковая мощность нижних конечностей, время реакции и спринтерские способности. Частоты встречаемости мутантных аллелей таких вариантов сравнивались с частотами в других популяциях Волго-Уральского региона. В геномах борцов найдено около 11 млн полиморфных локусов, в среднем 3,62 млн однонуклеотидных замен и 617 тыс инделов на геном. Из них 347 вариантов потенциально вызывают преждевременную терминацию трансляции белка. Корреляция со спортивными фенотипами была выявлена для 6 нонсенс-мутаций (гены ANKDD1B, SLC6A18, CCHCR1, VOPP1, ADAMTS12 и ZACN), в гомозиготном состоянии приводящих к достоверному изменению функциональных показателей спортсменов. У носителей замены p.Tyr319* (rs7447815) в гене SLC6A18 обнаружено снижение относительной пиковой мощности нижних конечностей. В то же время у борцов-татар была зарегистрирована меньшая частота мутантного аллеля в этом локусе по сравнению с башкирами и русскими. Также, согласно исследованиям GWAS, замена rs7447815 ассоциирована с риском развития остеоартроза и пониженной физической активностью. Количество полиморфных вариантов, найденных в геномах спортсменов, и доля нонсенс-мутаций в них соотносятся с результатами, описанными для других популяций. Нонсенс-мутация p.Tyr319* (rs7447815) в гене SLC6A18 является потенциальным маркером, ухудшающим значение относительной пиковой мощности нижних конечностей. The use of whole-genome sequencing technology provides extensive opportunities for the detection of new genetic markers that determine athletic performance. The aim of the study was to characterize the genome profile of high-class athletes and to identify genetic variants associated with some functional variables which can affect sports success. Materials and methods. For the first time, whole-genome sequencing of 20 professional belt wrestlers of Tatar nationality was carried out. Genetic variants were validated using microarray technology and/or imputation procedure. From the entire spectrum of variants those that were annotated as nonsense mutations, were found at the homozygous state and showed association with muscle mass, lower-extremity peak power, reaction time, and sprinting abilities were selected. The mutant allele frequencies of these variants were compared with the frequencies in other populations of the Volga-Ural region. Results. About 11 million polymorphic loci were found in the genomes of wrestlers, an average of 3.62 million single nucleotide polymorphisms and 617 thousand indels per genome. Of these, 347 variants potentially cause premature termination of protein translation. Correlation with sports phenotypes was found for 6 nonsense mutations (ANKDD1B, SLC6A18, CCHCR1, VOPP1, ADAMTS12, and ZACN genes), which in a homozygous state lead to significant changes in functional indicators of athletes. Wrestlers with p.Tyr319* (rs7447815) substitution in the SLC6A18 gene had decreased relative lower-extremity peak power. At the same time, a lower mutant allele frequency at this locus was registered in Tatar wrestlers compared to the Bashkirs and Russians. Also, according to the GWAS, the rs7447815 substitution is associated with the risk of osteoarthritis and decreased physical activity. Conclusions. The number of polymorphic variants found in the genomes of athletes and the proportion of nonsense mutations in them correlate with the results described for other populations. The nonsense mutation p.Tyr319* (rs7447815) in the SLC6A18 gene is a potential marker that reduces the relative peak power of the lower extremities.

Whole genome sequencing identifies genetic variants associated with co-trimoxazole hypersensitivity in Asians

2020 ◽  
Author(s):  
Chuang-Wei Wang ◽  
Wichittra Tassaneeyakul ◽  
Chun-Bing Chen ◽  
Wei-Ti Chen ◽  
Yu-Chuan Teng ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Whole Genome

scholarly journals 114 Whole genome sequencing to identify genetic variants underlying cardiovascular disease among Indian Asians

Heart ◽  
2012 ◽  
Vol 98 (Suppl 1) ◽  
pp. A64.1-A64 ◽  
Author(s):  
J C Chambers ◽  
S T Tan ◽  
W H Zhang ◽  
J Sehmi ◽  
A Al-Hussaini ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Whole Genome

scholarly journals Whole-genome sequencing reveals KRTAP1-1 as a novel genetic variant associated with antidepressant treatment outcomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jong-Ho Park ◽  
Shinn-Won Lim ◽  
Woojae Myung ◽  
Inho Park ◽  
Hyeok-Jae Jang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Treatment Outcomes ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Remission Rate ◽  
Antidepressant Treatment ◽  
Whole Genome ◽  
Loss Of Function

AbstractAchieving remission following initial antidepressant therapy in patients with major depressive disorder (MDD) is an important clinical result. Making predictions based on genetic markers holds promise for improving the remission rate. However, genetic variants found in previous genetic studies do not provide robust evidence to aid pharmacogenetic decision-making in clinical settings. Thus, the objective of this study was to perform whole-genome sequencing (WGS) using genomic DNA to identify genetic variants associated with the treatment outcomes of selective serotonin reuptake inhibitors (SSRIs). We performed WGS on 100 patients with MDD who were treated with escitalopram (discovery set: 36 remitted and 64 non-remitted). The findings were applied to an additional 553 patients with MDD who were treated with SSRIs (replication set: 185 remitted and 368 non-remitted). A novel loss-of-function variant (rs3213755) in keratin-associated protein 1–1 (KRTAP1-1) was identified in this study. This rs3213755 variant was significantly associated with remission following antidepressant treatment (p = 0.0184, OR 3.09, 95% confidence interval [CI] 1.22–7.80 in the discovery set; p = 0.00269, OR 1.75, 95% CI 1.22–2.53 in the replication set). Moreover, the expression level of KRTAP1-1 in surgically resected human temporal lobe samples was significantly associated with the rs3213755 genotype. WGS studies on a larger sample size in various ethnic groups are needed to investigate genetic markers useful in the pharmacogenetic prediction of remission following antidepressant treatment.

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