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AKBAROGHLI S, KOOSHAVAR D, GOLCHEHRE Z, KARAMZADE A, SABERI M, ALAEI MR, ABBASI SADEGH M, ASADOLLAHI M, KERAMATIPOUR M. Next-generation sequencing identified novel truncating mutations in BBS9 causing Bardet Biedl syndrome in two Iranian consanguineous families. IRANIAN JOURNAL OF CHILD NEUROLOGY 2022; 16:123-133. [PMID: 35222663 PMCID: PMC8753002 DOI: 10.22037/ijcn.v16i1.31650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Bardet-Biedl syndrome (BBS) is an autosomal recessive pleiotropic ciliopathy, which includes multi-organ clinical manifestations. The known genes involved in the development of the disease account for the causality in about 80% of the examined cases. MATERIALS & METHODS We investigated two Iranian unrelated clinically diagnosed BBS patients, using a targeted next-generation sequencing panel consisting of 18 known BBS genes. The detected variants were investigated in the pedigree and studied using in silico tools for their pathogenicity. Patients' phenotypes were also assessed. RESULTS Novel homozygous variants were detected in BBS9 gene in each patient, c.2014C>T, p.Gln672Ter and c.673_674insAA, p.Gln225GlnfsX10. The variants were segregated in the corresponding pedigree and were authenticated to obtain enough evidence to be categorized as pathogenic variants. CONCLUSION Patients with truncating mutations in the same gene seem to show similar phenotypic features. Detection of novel and family-specific mutations is typically expected in the genetic hereditary diseases in Iran, which can finally lead to prevent the recurrence of the disease in the consanguineous marriages.
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Affiliation(s)
- Susan AKBAROGHLI
- Department of Pediatrics, Mofid Children’s Hospital, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Daniz KOOSHAVAR
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra GOLCHEHRE
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arezou KARAMZADE
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad SABERI
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza ALAEI
- Department of Pediatrics, Mofid Children’s Hospital, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud ABBASI SADEGH
- Department of Pediatrics, Mofid Children’s Hospital, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa ASADOLLAHI
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad KERAMATIPOUR
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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A Novel BBS9 Mutation Identified via Whole-Exome Sequencing in a Chinese Family with Bardet-Biedl Syndrome. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4514967. [PMID: 34692830 PMCID: PMC8536422 DOI: 10.1155/2021/4514967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a genetically heterogeneous disorder characterized by polydactyly, obesity, rod-cone dystrophy, and mental retardation. Twenty-one genes have been identified as causing BBS. This study collected a BBS pedigree from two patients and performed whole-exome sequencing on one patient. We identified a novel homozygous variant c.1114C>T (p.Q372X) in the BBS9 of the two siblings. This variant was confirmed and completely cosegregated with the disease of this family by Sanger sequencing. We report a novel homozygous variant c.1114C>T in the BBS9 gene in a Chinese family.
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Identification of a Novel Homozygous Missense (c.443A>T:p.N148I) Mutation in BBS2 in a Kashmiri Family with Bardet-Biedl Syndrome. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6626015. [PMID: 33688495 PMCID: PMC7925018 DOI: 10.1155/2021/6626015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/31/2020] [Accepted: 01/31/2021] [Indexed: 11/17/2022]
Abstract
Background Bardet-Biedl syndrome (BBS) is a rare autosomal recessive inherited disorder with distinctive clinical feature such as obesity, degeneration of retina, polydactyly, and renal abnormalities. The study was aimed at finding out the disease-causing variant/s in patients exhibiting clinical features of BBS. Methods The identification of disease-causing variant was done by using whole exome sequencing on Illumina HiSeq 4000 platform involving the SeqCap EZ Exome v3 kit (Roche NimbleGen). The identified variant was further validated by Sanger sequencing. Results WES revealed a novel homozygous missense mutation (NM_031885: c.443A>T:p.N148I) in exon 3 of the BBS2 gene. Sanger sequencing confirmed this variant as homozygous in both affected subjects and heterozygous in obligate parents, demonstrating autosomal recessive inheritance pattern. To the best of our knowledge, this variant was not present in literature and all publically available databases. The candidate variant is predicted to be pathogenic by a set of in-silico softwares. Conclusion Clinical and genetic spectrum of BBS and BBS-like disorders is not completely defined in the Pakistani as well as in Kashmiri population. Therefore, more comprehensive genetic studies are required to gain insights into genotype-phenotype associations to facilitate carrier screening and genetic counseling of families with such disorders.
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Jia M, Li X, Jiang C, Wang K, Zuo T, He G, Qin L, Xu W. Testis-enriched circular RNA circ-Bbs9 plays an important role in Leydig cell proliferation by regulating a CyclinD2-dependent pathway. Reprod Fertil Dev 2021; 32:355-362. [PMID: 31708014 DOI: 10.1071/rd18474] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/01/2019] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs belong to a new category of non-coding RNAs, characterised by a circular structure, conservation, stability and high expression in eukaryotes. They often show tissue- or cell-specific expression. Here, we identified a testis-enriched circular RNA (circRNA), circular Bbs9 (circ-Bbs9) that is highly expressed in mouse testis. An RNase R treatment experiment confirmed that circ-Bbs9 is indeed a circRNA. In situ hybridisation experiments showed that circ-Bbs9 is expressed in Leydig cells along seminiferous tubules and in the cytoplasm of the TM3 Leydig cell line. Knocking down the circ-Bbs9 in TM3 cells by lentivirus vectors arrested cell proliferation, whereas overexpression of circ-Bbs9 induced cell proliferation significantly. Knocking down circ-Bbs9 inhibited the protein level of cyclin D2 (Ccnd2) and RNA immunoprecipitation results showed that circ-Bbs9 interacts with Ccnd2. Our results show that use of the Hedgehog pathway Smoothened Agonist (SAG) HCl and antagonists cyclopamine and gant6 affects the expression levels of Glioma-Associated Oncogene Homolog 1 (Gli1), Ccnd2 and other genes in this pathway. Our research reveals that a Leydig cell-specific circRNA, circ-Bbs9, plays a critical role in Leydig cell proliferation through regulating the levels of cell cycle-related Ccnd2. Thus, our results emphasise the important role of circRNA in the male reproductive system.
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Affiliation(s)
- Minzhi Jia
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xiaoliang Li
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Chuan Jiang
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Ke Wang
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Tao Zuo
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Guolin He
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Lang Qin
- Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China; and Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China; and Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Wenming Xu
- Joint Laboratory of Reproductive Medicine, SCU-CUHK, Key Laboratory of Obstetric, Gynaecologic and Paediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China; and Department of Obstetrics and Gynaecology, West China Second University Hospital, Sichuan University, Chengdu 610041, P. R. China; and Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
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Niazi RK, Gjesing AP, Hollensted M, Have CT, Borisevich D, Grarup N, Pedersen O, Ullah A, Shahid G, Shafqat I, Gul A, Hansen T. Screening of 31 genes involved in monogenic forms of obesity in 23 Pakistani probands with early-onset childhood obesity: a case report. BMC MEDICAL GENETICS 2019; 20:152. [PMID: 31488071 PMCID: PMC6727494 DOI: 10.1186/s12881-019-0886-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/29/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND Consanguine families display a high degree of homozygosity which increases the risk of family members suffering from autosomal recessive disorders. Thus, homozygous mutations in monogenic obesity genes may be a more frequent cause of childhood obesity in a consanguineous population. METHODS We identified 23 probands from 23 Pakistani families displaying autosomal recessive obesity. We have previously excluded mutations in MC4R, LEP and LEPR in all probands. Using a chip-based, target-region capture array, 31 genes involved in monogenic forms of obesity, were screened in all probands. RESULTS We identified 31 rare non-synonymous possibly pathogenic variants (28 missense and three nonsense) within the 31 selected genes. All variants were heterozygous, thus no homozygous pathogenic variants were found. Two of the rare heterozygous nonsense variants identified (p.R75X and p.R481X) were found in BBS9 within one proband, suggesting that obesity is caused by compound heterozygosity. Sequencing of the parents supported the compound heterozygous nature of obesity as each parent was carrying one of the variants. Subsequent clinical investigation strongly indicated that the proband had Bardet-Biedl syndrome. CONCLUSIONS Mutation screening in 31 genes among probands with severe early-onset obesity from Pakistani families did not reveal the presence of homozygous obesity causing variants. However, a compound heterozygote carrier of BBS9 mutations was identified, indicating that compound heterozygosity must not be overlooked when investigating the genetic etiology of severe childhood obesity in populations with a high degree of consanguinity.
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Affiliation(s)
- Robina Khan Niazi
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Children Hospital, Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Anette Prior Gjesing
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Hollensted
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Theil Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dmitrii Borisevich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Asmat Ullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, PIMS, Islamabad, Pakistan
| | - Gulbin Shahid
- Children Hospital, Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Ifrah Shafqat
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Muzammal M, Zubair M, Bierbaumer S, Blatterer J, Graf R, Gul A, Abbas S, Badar M, Abbasi AA, Khan MA, Windpassinger C. Exome sequence analysis in consanguineous Pakistani families inheriting Bardet-Biedle syndrome determined founder effect of mutation c.299delC (p.Ser100Leufs*24) in BBS9 gene. Mol Genet Genomic Med 2019; 7:e834. [PMID: 31294530 PMCID: PMC6687644 DOI: 10.1002/mgg3.834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/11/2019] [Accepted: 05/22/2019] [Indexed: 12/29/2022] Open
Abstract
Background Bardet‐Biedl syndrome (BBS) is characterized by a heterogeneous phenotypic spectrum of retinopathy, intellectual disability (ID), obesity, polydactyly, and kidney dysfunctions as the major clinical features. Genetic investigations have reported 21 BBS genes, the products of which are mostly located at the centrosome, basal body or the ciliary transition zone. Methods In the present genetic report, we analyzed two apparently unrelated consanguineous BBS families from Dera Ismail Khan (D.I.Khan) district, Pakistan. Genetic mapping was performed using Whole exome sequencing and Sanger sequencing. Results Whole exome sequencing identified a recently reported single base deletion NM_001033604.1:c.299delC in the fourth exon of BBS9 in both families. The identified frameshift mutation is predicted to cause premature truncation of the expressed protein (p.Ser100Leufs*24). This mutation has previously been mapped in a consanguineous Pakistani family; therefore this is the second report of this particular mutation in two additional BBS families originating from different locations. Conclusion We speculate the evolutionary significance of this mutation and assume its strong founder effect in the Khaisoori tribe of D.I.Khan. Based on these findings, we suggest developing a molecular diagnostic test that may be used for premarital and prenatal screening of families at risk of BBS.
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Affiliation(s)
- Muhammad Muzammal
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Zubair
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Sophie Bierbaumer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jasmin Blatterer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ricarda Graf
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Aisha Gul
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Safdar Abbas
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Muhammad Badar
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Ansar Ahmad Abbasi
- Department of Zoology, Mirpur University of Science and Technology (MUST), Mirpur, Pakistan
| | - Muzammil Ahmad Khan
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
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Novel splicing variant c. 208+2T>C in BBS5 segregates with Bardet-Biedl syndrome in an Iranian family by targeted exome sequencing. Biosci Rep 2019; 39:BSR20181544. [PMID: 30850397 PMCID: PMC6438871 DOI: 10.1042/bsr20181544] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 01/13/2023] Open
Abstract
Bardet–Biedl syndrome (BBS) is a rare genetically heterogeneous ciliopathy which accompanies retinitis pigmentosa (RP). However, the BBS5 mutation remains unclear in Iranians with BBS. The purpose of study is to evaluate genetic analyses of a BBS Iranian family using targetted exome sequencing (TES). A male 11-year-old proband and three related family members were recruited. Biochemical tests, electrocardiography and visual acuity testing, such as funduscopic, fundus photography (FP), optical coherence tomography (OCT), and standard electroretinography, were conducted. Molecular analysis and high-throughput DNA sequence analysis were performed. The proband was diagnosed with possible BBS based on the presence of three primary features and two secondary features. The TES analysis of the proband with BBS resulted in the identification of a novel, homozygous splicing variant c. 208+2T>C of the BBS5 gene (NM_152384.2) in this Iranian BBS family. This variant was confirmed and was completely co-segregated with the disease in this family by Sanger sequencing. Thus, we report a novel, homozygous splicing site variant c.208+2T>C in the BBS5 gene for the first time in the Iranian family.
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Córdova-Fletes C, Becerra-Solano LE, Rangel-Sosa MM, Rivas-Estilla AM, Alberto Galán-Huerta K, Ortiz-López R, Rojas-Martínez A, Juárez-Vázquez CI, García-Ortiz JE. Uncommon runs of homozygosity disclose homozygous missense mutations in two ciliopathy-related genes ( SPAG17 and WDR35 ) in a patient with multiple brain and skeletal anomalies. Eur J Med Genet 2018; 61:161-167. [DOI: 10.1016/j.ejmg.2017.11.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
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Pigeyre M, Saqlain M, Turcotte M, Raja GK, Meyre D. Obesity genetics: insights from the Pakistani population. Obes Rev 2018; 19:364-380. [PMID: 29265593 DOI: 10.1111/obr.12644] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 01/26/2023]
Abstract
The Pakistani population is extensively diverse, indicating a genetic admixture of European and Central/West Asian migrants with indigenous South Asian gene pools. Pakistanis are organized in different ethnicities/castes based on cultural, linguistic and geographical origin. While Pakistan is facing a rapid nutritional transition, the rising prevalence of obesity is driving a growing burden of health complications and mortality. This represents a unique opportunity for the research community to study the interplay between obesogenic environmental changes and obesity predisposing genes in the time frame of one generation. This review recapitulates the ancestral origins of Pakistani population, the societal determinants of the rise in obesity and its governmental management. We describe the contribution of syndromic, monogenic non-syndromic and polygenic obesity genes identified in the Pakistani population. We then discuss the utility of gene identification approaches based on large consanguineous families and original gene × environment interaction study designs in discovering new obesity genes and causal pathways. Elucidation of the genetic basis of obesity in the Pakistani population may result in improved methods of obesity prevention and treatment globally.
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Affiliation(s)
- M Pigeyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Nutrition, CHRU Lille, University of Lille, Lille, France
| | - M Saqlain
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - M Turcotte
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - G K Raja
- Department of Biochemistry, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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Derks MFL, Megens HJ, Bosse M, Lopes MS, Harlizius B, Groenen MAM. A systematic survey to identify lethal recessive variation in highly managed pig populations. BMC Genomics 2017; 18:858. [PMID: 29121877 PMCID: PMC5680825 DOI: 10.1186/s12864-017-4278-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/03/2017] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Lethal recessive variation can cause prenatal death of homozygous offspring. Although usually present at low-frequency in populations, the impact on individual fitness can be substantial. Until recently, the presence of recessive embryonic lethal variation could only be measured indirectly through reduced fertility. In this study, we estimate the presence of genetic loci associated with both early and late termination of development during gestation in pigs from the wealth of genome data routinely generated by a commercial breeding company. RESULTS We examined three commercial pig (Sus scrofa) populations for potentially deleterious genetic variation based on 80 K SNP-chip genotypes, and estimate the effects on reproductive traits. 24,000 pigs from three populations were analyzed for missing or depletion of homozygous haplotypes. We identified 145 haplotypes (ranging from 0.5-4 Mb in size) in the genome with complete absence or depletion of homozygous animals. Thirty-five haplotypes show a negative effect on at least one of the analysed reproductive traits (total number born, number of stillborn, and number of mummified piglets). One variant in particular appeared to result in relative late termination of development of fetuses, responsible for a significant fraction of observed stillborn piglets ('mummies'), as they die mid-gestation. Moreover, we identified the BMPER gene as a likely candidate underlying this phenomenon. CONCLUSIONS Our study shows that although lethal recessive variation is present, the frequency of these alleles is invariably low in these highly managed populations. Nevertheless, due to cumulative effects of deleterious variants, large numbers of affected offspring are produced. Furthermore, our study demonstrates the use of a large-scale commercial genetic experiment to systematically screen for 'natural knockouts' that can increase understanding of gene function.
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Affiliation(s)
- Martijn F L Derks
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
| | - Hendrik-Jan Megens
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Mirte Bosse
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Marcos S Lopes
- Topigs Norsvin Research Center, Beuningen, the Netherlands.,Topigs Norsvin, Curitiba, Brazil
| | | | - Martien A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
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Niche harmony search algorithm for detecting complex disease associated high-order SNP combinations. Sci Rep 2017; 7:11529. [PMID: 28912584 PMCID: PMC5599559 DOI: 10.1038/s41598-017-11064-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 08/17/2017] [Indexed: 02/01/2023] Open
Abstract
Genome-wide association study is especially challenging in detecting high-order disease-causing models due to model diversity, possible low or even no marginal effect of the model, and extraordinary search and computations. In this paper, we propose a niche harmony search algorithm where joint entropy is utilized as a heuristic factor to guide the search for low or no marginal effect model, and two computationally lightweight scores are selected to evaluate and adapt to diverse of disease models. In order to obtain all possible suspected pathogenic models, niche technique merges with HS, which serves as a taboo region to avoid HS trapping into local search. From the resultant set of candidate SNP-combinations, we use G-test statistic for testing true positives. Experiments were performed on twenty typical simulation datasets in which 12 models are with marginal effect and eight ones are with no marginal effect. Our results indicate that the proposed algorithm has very high detection power for searching suspected disease models in the first stage and it is superior to some typical existing approaches in both detection power and CPU runtime for all these datasets. Application to age-related macular degeneration (AMD) demonstrates our method is promising in detecting high-order disease-causing models.
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12
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Kaur Y, de Souza RJ, Gibson WT, Meyre D. A systematic review of genetic syndromes with obesity. Obes Rev 2017; 18:603-634. [PMID: 28346723 DOI: 10.1111/obr.12531] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
Syndromic monogenic obesity typically follows Mendelian patterns of inheritance and involves the co-presentation of other characteristics, such as mental retardation, dysmorphic features and organ-specific abnormalities. Previous reviews on obesity have reported 20 to 30 syndromes but no systematic review has yet been conducted on syndromic obesity. We searched seven databases using terms such as 'obesity', 'syndrome' and 'gene' to conduct a systematic review of literature on syndromic obesity. Our literature search identified 13,719 references. After abstract and full-text review, 119 relevant papers were eligible, and 42 papers were identified through additional searches. Our analysis of these 161 papers found that 79 obesity syndromes have been reported in literature. Of the 79 syndromes, 19 have been fully genetically elucidated, 11 have been partially elucidated, 27 have been mapped to a chromosomal region and for the remaining 22, neither the gene(s) nor the chromosomal location(s) have yet been identified. Interestingly, 54.4% of the syndromes have not been assigned a name, whereas 13.9% have more than one name. We report on organizational inconsistencies (e.g. naming discrepancies and syndrome classification) and provide suggestions for improvements. Overall, this review illustrates the need for increased clinical and genetic research on syndromes with obesity.
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Affiliation(s)
- Y Kaur
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - W T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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13
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Maria M, Lamers IJC, Schmidts M, Ajmal M, Jaffar S, Ullah E, Mustafa B, Ahmad S, Nazmutdinova K, Hoskins B, van Wijk E, Koster-Kamphuis L, Khan MI, Beales PL, Cremers FPM, Roepman R, Azam M, Arts HH, Qamar R. Genetic and clinical characterization of Pakistani families with Bardet-Biedl syndrome extends the genetic and phenotypic spectrum. Sci Rep 2016; 6:34764. [PMID: 27708425 PMCID: PMC5052523 DOI: 10.1038/srep34764] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/09/2016] [Indexed: 11/29/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive disorder that is both genetically and clinically heterogeneous. To date 19 genes have been associated with BBS, which encode proteins active at the primary cilium, an antenna-like organelle that acts as the cell’s signaling hub. In the current study, a combination of mutation screening, targeted sequencing of ciliopathy genes associated with BBS, and whole-exome sequencing was used for the genetic characterization of five families including four with classic BBS symptoms and one BBS-like syndrome. This resulted in the identification of novel mutations in BBS genes ARL6 and BBS5, and recurrent mutations in BBS9 and CEP164. In the case of CEP164, this is the first report of two siblings with a BBS-like syndrome with mutations in this gene. Mutations in this gene were previously associated with nephronophthisis 15, thus the current results expand the CEP164-associated phenotypic spectrum. The clinical and genetic spectrum of BBS and BBS-like phenotypes is not fully defined in Pakistan. Therefore, genetic studies are needed to gain insights into genotype-phenotype correlations, which will in turn improve the clinician’s ability to make an early and accurate diagnosis, and facilitate genetic counseling, leading to directly benefiting families with affected individuals.
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Affiliation(s)
- Maleeha Maria
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ideke J C Lamers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Miriam Schmidts
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.,Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK.,Center for Pediatrics and Adolescent Medicine, Pediatric Genetics Division, University Hospital Freiburg, Germany
| | - Muhammad Ajmal
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | | | - Ehsan Ullah
- School of Applied Sciences, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand.,Auckland City Hospital, Auckland District Health Board, Auckland, New Zealand
| | - Bilal Mustafa
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Shakeel Ahmad
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Katia Nazmutdinova
- Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK
| | - Bethan Hoskins
- North East Thames Regional Genetics Service, Hospital for Children, London, UK
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands.,Donders Center for Neurosciences, Radboud University Nijmegen, the Netherlands
| | - Linda Koster-Kamphuis
- Department of Pediatric Nephrology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Phil L Beales
- Genetics and Genomic Medicine, UCL Institute of Child Health, 30 Guilford Street, London, UK.,Centre for Translational Omics-GOSgene, Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Donders Center for Neurosciences, Radboud University Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Maleeha Azam
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Heleen H Arts
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.,Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Department of Biochemistry, Al-Nafees Medical College &Hospital, Isra University, Islamabad, Pakistan.,Pakistan Academy of Sciences, Constitution Avenue, Islamabad, Pakistan
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