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Pipal KV, Mamtani M, Patel AA, Jaiswal SG, Jaisinghani MT, Kulkarni H. Susceptibility Loci for Type 2 Diabetes in the Ethnically Endogamous Indian Sindhi Population: A Pooled Blood Genome-Wide Association Study. Genes (Basel) 2022; 13:genes13081298. [PMID: 35893037 PMCID: PMC9331904 DOI: 10.3390/genes13081298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 12/10/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex metabolic derangement that has a strong genetic basis. There is substantial population-specificity in the association of genetic variants with T2D. The Indian urban Sindhi population is at a high risk of T2D. The genetic basis of T2D in this population is unknown. We interrogated 28 pooled whole blood genomes of 1402 participants from the Diabetes In Sindhi Families In Nagpur (DISFIN) study using Illumina’s Global Screening Array. From a total of 608,550 biallelic variants, 140 were significantly associated with T2D after adjusting for comorbidities, batch effects, pooling error, kinship status and pooling variation in a random effects multivariable logistic regression framework. Of the 102 well-characterized genes that these variants mapped onto, 70 genes have been previously reported to be associated with T2D to varying degrees with known functional relevance. Excluding open reading frames, intergenic non-coding elements and pseudogenes, our study identified 22 novel candidate genes in the Sindhi population studied. Our study thus points to the potential, interesting candidate genes associated with T2D in an ethnically endogamous population. These candidate genes need to be fully investigated in future studies.
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Affiliation(s)
- Kanchan V. Pipal
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Manju Mamtani
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
- M&H Research, LLC, San Antonio, TX 78249, USA
| | - Ashwini A. Patel
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Sujeet G. Jaiswal
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Manisha T. Jaisinghani
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
| | - Hemant Kulkarni
- Lata Medical Research Foundation, Nagpur 440002, India; (K.V.P.); (M.M.); (A.A.P.); (S.G.J.); (M.T.J.)
- M&H Research, LLC, San Antonio, TX 78249, USA
- Correspondence:
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Liu Y, Qu HQ, Chang X, Qu J, Mentch FD, Nguyen K, Tian L, Glessner J, Sleiman PMA, Hakonarson H. Mutation Burden Analysis of Six Common Mental Disorders in African Americans by Whole Genome Sequencing. Hum Mol Genet 2022; 31:3769-3776. [PMID: 35642741 DOI: 10.1093/hmg/ddac129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
Mental disorders present a global health concern, with limited treatment options. In today's medical practice, medications such as antidepressants are prescribed not only for depression, but also for conditions such as anxiety and attention deficit hyperactivity disorder (ADHD). Therefore, identifying gene targets for specific disorders is important and offers improved precision. In this study, we performed a genetic analysis of six common mental disorders, ADHD, anxiety, depression, delays in mental developments, intellectual disabilities (ID), and speech/language disorder in the ethnic minority of African Americans (AA) using whole genome sequencing (WGS). WGS data was generated from blood-derived DNA from 4178 AA individuals, including 1384 patients with the diagnosis of at least one mental disorder. Mutation burden analysis was applied based on rare and deleterious mutations in the AA population between cases and controls, and further analyzed in the context of patients with single mental disorder diagnosis. Certain genes uncovered demonstrated significant p values in mutation burden analysis. In addition, exclusive recurrences in specific type of disorder were scanned through gene-drug interaction databases to assess for availability of potential medications. We uncovered 15 genes harboring deleterious mutations, including HMGCR and UST for ADHD; FNTB for anxiety, XIRP2, NPPC, , STK33, PANX1 and NTS for depression; RUNX3, TACR1, and NDUFS7 for delays in mental developments; HPN for ID; COL6A3, DDB1, and NDUFA11 for speech/language disorder. Taken together, we have established critical insight into the development of new precision medicine approaches for mental disorders in African Americans.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Jingchun Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Kenny Nguyen
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
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