1
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Townsend J, Braz CU, Taylor T, Khatib H. Effects of paternal methionine supplementation on sperm DNA methylation and embryo transcriptome in sheep. ENVIRONMENTAL EPIGENETICS 2022; 9:dvac029. [PMID: 36727109 PMCID: PMC9885981 DOI: 10.1093/eep/dvac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/18/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Environmental effects on gene expression and offspring development can be mediated by epigenetic modifications. It is well established that maternal diet influences DNA methylation patterns and phenotypes in the offspring; however, the epigenetic effects of paternal diet on developing offspring warrants further investigation. Here, we examined how a prepubertal methionine-enriched paternal diet affected sperm DNA methylation and its subsequent effects on embryo gene expression. Three treatment and three control rams were bred to seven ewes, and blastocysts were flushed for RNA extraction. Semen was collected from all rams and submitted for reduced representation bisulfite sequencing analysis. In total, 166 differentially methylated cytosines were identified in the sperm from treatment versus control rams. Nine genes were found to be differentially expressed in embryos produced from treatment versus control rams, and seven differentially methylated cytosines in the sperm were found to be highly correlated with gene expression in the embryos. Our results demonstrate that sperm methylation differences induced by diet may influence fetal programming.
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Affiliation(s)
- Jessica Townsend
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Camila U Braz
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Todd Taylor
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Dr., Madison, WI 53706, USA
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2
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Mizumoto S, Yamada S. Congenital Disorders of Deficiency in Glycosaminoglycan Biosynthesis. Front Genet 2021; 12:717535. [PMID: 34539746 PMCID: PMC8446454 DOI: 10.3389/fgene.2021.717535] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/12/2021] [Indexed: 12/04/2022] Open
Abstract
Glycosaminoglycans (GAGs) including chondroitin sulfate, dermatan sulfate, and heparan sulfate are covalently attached to specific core proteins to form proteoglycans, which are distributed at the cell surface as well as in the extracellular matrix. Proteoglycans and GAGs have been demonstrated to exhibit a variety of physiological functions such as construction of the extracellular matrix, tissue development, and cell signaling through interactions with extracellular matrix components, morphogens, cytokines, and growth factors. Not only connective tissue disorders including skeletal dysplasia, chondrodysplasia, multiple exostoses, and Ehlers-Danlos syndrome, but also heart and kidney defects, immune deficiencies, and neurological abnormalities have been shown to be caused by defects in GAGs as well as core proteins of proteoglycans. These findings indicate that GAGs and proteoglycans are essential for human development in major organs. The glycobiological aspects of congenital disorders caused by defects in GAG-biosynthetic enzymes including specific glysocyltransferases, epimerases, and sulfotransferases, in addition to core proteins of proteoglycans will be comprehensively discussed based on the literature to date.
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Affiliation(s)
- Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
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3
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Unger CM, Devine J, Hallgrímsson B, Rolian C. Selection for increased tibia length in mice alters skull shape through parallel changes in developmental mechanisms. eLife 2021; 10:e67612. [PMID: 33899741 PMCID: PMC8118654 DOI: 10.7554/elife.67612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 12/18/2022] Open
Abstract
Bones in the vertebrate cranial base and limb skeleton grow by endochondral ossification, under the control of growth plates. Mechanisms of endochondral ossification are conserved across growth plates, which increases covariation in size and shape among bones, and in turn may lead to correlated changes in skeletal traits not under direct selection. We used micro-CT and geometric morphometrics to characterize shape changes in the cranium of the Longshanks mouse, which was selectively bred for longer tibiae. We show that Longshanks skulls became longer, flatter, and narrower in a stepwise process. Moreover, we show that these morphological changes likely resulted from developmental changes in the growth plates of the Longshanks cranial base, mirroring changes observed in its tibia. Thus, indirect and non-adaptive morphological changes can occur due to developmental overlap among distant skeletal elements, with important implications for interpreting the evolutionary history of vertebrate skeletal form.
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Affiliation(s)
- Colton M Unger
- Department of Biological Sciences, University of CalgaryCalgaryCanada
- McCaig Institute for Bone and Joint HealthCalgaryCanada
| | - Jay Devine
- Department of Cell Biology and Anatomy, University of CalgaryCalgaryCanada
| | - Benedikt Hallgrímsson
- McCaig Institute for Bone and Joint HealthCalgaryCanada
- Department of Cell Biology and Anatomy, University of CalgaryCalgaryCanada
- Alberta Children's Hospital Research Institute for Child and Maternal Health, University of CalgaryCalgaryCanada
| | - Campbell Rolian
- McCaig Institute for Bone and Joint HealthCalgaryCanada
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of CalgaryCalgaryCanada
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4
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Paganini C, Gramegna Tota C, Superti-Furga A, Rossi A. Skeletal Dysplasias Caused by Sulfation Defects. Int J Mol Sci 2020; 21:ijms21082710. [PMID: 32295296 PMCID: PMC7216085 DOI: 10.3390/ijms21082710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/18/2022] Open
Abstract
Proteoglycans (PGs) are macromolecules present on the cell surface and in the extracellular matrix that confer specific mechanical, biochemical, and physical properties to tissues. Sulfate groups present on glycosaminoglycans, linear polysaccharide chains attached to PG core proteins, are fundamental for correct PG functions. Indeed, through the negative charge of sulfate groups, PGs interact with extracellular matrix molecules and bind growth factors regulating tissue structure and cell behavior. The maintenance of correct sulfate metabolism is important in tissue development and function, particularly in cartilage where PGs are fundamental and abundant components of the extracellular matrix. In chondrocytes, the main sulfate source is the extracellular space, then sulfate is taken up and activated in the cytosol to the universal sulfate donor to be used in sulfotransferase reactions. Alteration in each step of sulfate metabolism can affect macromolecular sulfation, leading to the onset of diseases that affect mainly cartilage and bone. This review presents a panoramic view of skeletal dysplasias caused by mutations in genes encoding for transporters or enzymes involved in macromolecular sulfation. Future research in this field will contribute to the understanding of the disease pathogenesis, allowing the development of targeted therapies aimed at alleviating, preventing, or modifying the disease progression.
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Affiliation(s)
- Chiara Paganini
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, 27100 Pavia, Italy; (C.P.); (C.G.T.)
| | - Chiara Gramegna Tota
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, 27100 Pavia, Italy; (C.P.); (C.G.T.)
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
| | - Antonio Rossi
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, 27100 Pavia, Italy; (C.P.); (C.G.T.)
- Correspondence:
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5
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Nissim S, Leshchiner I, Mancias JD, Greenblatt MB, Maertens O, Cassa CA, Rosenfeld JA, Cox AG, Hedgepeth J, Wucherpfennig JI, Kim AJ, Henderson JE, Gonyo P, Brandt A, Lorimer E, Unger B, Prokop JW, Heidel JR, Wang XX, Ukaegbu CI, Jennings BC, Paulo JA, Gableske S, Fierke CA, Getz G, Sunyaev SR, Wade Harper J, Cichowski K, Kimmelman AC, Houvras Y, Syngal S, Williams C, Goessling W. Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer. Nat Genet 2019; 51:1308-1314. [PMID: 31406347 DOI: 10.1038/s41588-019-0475-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
Pancreatic ductal adenocarcinoma is an aggressive cancer with limited treatment options1. Approximately 10% of cases exhibit familial predisposition, but causative genes are not known in most families2. We perform whole-genome sequence analysis in a family with multiple cases of pancreatic ductal adenocarcinoma and identify a germline truncating mutation in the member of the RAS oncogene family-like 3 (RABL3) gene. Heterozygous rabl3 mutant zebrafish show increased susceptibility to cancer formation. Transcriptomic and mass spectrometry approaches implicate RABL3 in RAS pathway regulation and identify an interaction with RAP1GDS1 (SmgGDS), a chaperone regulating prenylation of RAS GTPases3. Indeed, the truncated mutant RABL3 protein accelerates KRAS prenylation and requires RAS proteins to promote cell proliferation. Finally, evidence in patient cohorts with developmental disorders implicates germline RABL3 mutations in RASopathy syndromes. Our studies identify RABL3 mutations as a target for genetic testing in cancer families and uncover a mechanism for dysregulated RAS activity in development and cancer.
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Affiliation(s)
- Sahar Nissim
- Gastroenterology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA.,Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA
| | - Ignaty Leshchiner
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joseph D Mancias
- Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine and the Hospital for Special Surgery, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Ophélia Maertens
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher A Cassa
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jill A Rosenfeld
- The Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Andrew G Cox
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - John Hedgepeth
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Julia I Wucherpfennig
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew J Kim
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jake E Henderson
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick Gonyo
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Anthony Brandt
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ellen Lorimer
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Bethany Unger
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry R Heidel
- Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | | | | | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | | | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Gad Getz
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Cancer Center and Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Shamil R Sunyaev
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Karen Cichowski
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alec C Kimmelman
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Yariv Houvras
- Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY, USA
| | - Sapna Syngal
- Gastroenterology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
| | - Carol Williams
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wolfram Goessling
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Dana-Farber Cancer Institute, Boston, MA, USA. .,Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA. .,The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Harvard Stem Cell Institute, Cambridge, MA, USA. .,Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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6
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An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. NPJ Genom Med 2018; 3:21. [PMID: 30131872 PMCID: PMC6089983 DOI: 10.1038/s41525-018-0060-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/06/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Despite major progress in defining the genetic basis of Mendelian disorders, the molecular etiology of many cases remains unknown. Patients with these undiagnosed disorders often have complex presentations and require treatment by multiple health care specialists. Here, we describe an integrated clinical diagnostic and research program using whole-exome and whole-genome sequencing (WES/WGS) for Mendelian disease gene discovery. This program employs specific case ascertainment parameters, a WES/WGS computational analysis pipeline that is optimized for Mendelian disease gene discovery with variant callers tuned to specific inheritance modes, an interdisciplinary crowdsourcing strategy for genomic sequence analysis, matchmaking for additional cases, and integration of the findings regarding gene causality with the clinical management plan. The interdisciplinary gene discovery team includes clinical, computational, and experimental biomedical specialists who interact to identify the genetic etiology of the disease, and when so warranted, to devise improved or novel treatments for affected patients. This program effectively integrates the clinical and research missions of an academic medical center and affords both diagnostic and therapeutic options for patients suffering from genetic disease. It may therefore be germane to other academic medical institutions engaged in implementing genomic medicine programs.
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7
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Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Res 2018; 28:423-431. [PMID: 29567674 PMCID: PMC5880234 DOI: 10.1101/gr.223693.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 02/21/2018] [Indexed: 12/30/2022]
Abstract
Over a decade ago, the Atacama humanoid skeleton (Ata) was discovered in the Atacama region of Chile. The Ata specimen carried a strange phenotype-6-in stature, fewer than expected ribs, elongated cranium, and accelerated bone age-leading to speculation that this was a preserved nonhuman primate, human fetus harboring genetic mutations, or even an extraterrestrial. We previously reported that it was human by DNA analysis with an estimated bone age of about 6-8 yr at the time of demise. To determine the possible genetic drivers of the observed morphology, DNA from the specimen was subjected to whole-genome sequencing using the Illumina HiSeq platform with an average 11.5× coverage of 101-bp, paired-end reads. In total, 3,356,569 single nucleotide variations (SNVs) were found as compared to the human reference genome, 518,365 insertions and deletions (indels), and 1047 structural variations (SVs) were detected. Here, we present the detailed whole-genome analysis showing that Ata is a female of human origin, likely of Chilean descent, and its genome harbors mutations in genes (COL1A1, COL2A1, KMT2D, FLNB, ATR, TRIP11, PCNT) previously linked with diseases of small stature, rib anomalies, cranial malformations, premature joint fusion, and osteochondrodysplasia (also known as skeletal dysplasia). Together, these findings provide a molecular characterization of Ata's peculiar phenotype, which likely results from multiple known and novel putative gene mutations affecting bone development and ossification.
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Affiliation(s)
- Sanchita Bhattacharya
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Jian Li
- Roche Sequencing Solutions, Belmont, California 94002, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Matthew J Kan
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Felice A Bava
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Shann-Ching Chen
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico (UNAM) Santiago de Querétaro, Querétaro 76230, Mexico
| | - Xuhuai Ji
- Human Immune Monitoring Center and Functional Genomics Facility, Stanford University, Stanford, California 94305, USA
| | - Emery Smith
- Ultra Intelligence Corporation, Boulder, Colorado 80301, USA
| | - Narges B Asadi
- Roche Sequencing Solutions, Belmont, California 94002, USA
| | - Ralph S Lachman
- Department of Pediatric Radiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hugo Y K Lam
- Roche Sequencing Solutions, Belmont, California 94002, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Garry P Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
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8
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Shabbir RMK, Nalbant G, Ahmad N, Malik S, Tolun A. Homozygous CHST11 mutation in chondrodysplasia, brachydactyly, overriding digits, clino-symphalangism and synpolydactyly. J Med Genet 2018. [PMID: 29514872 DOI: 10.1136/jmedgenet-2017-105003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Carbohydrate sulfotransferase 11 (CHST11) is a membrane protein of Golgi that catalyses the transfer of sulfate to position 4 of the N-acetylgalactosamine residues of chondroitin. Chondroitin sulfate is the predominant proteoglycan in cartilage, and its sulfation is important in the developing growth plate of cartilage. A homozygous deletion encompassing part of the gene and the embedded miRNA MIR3922 had been detected in a woman with hand/foot malformation and malignant lymphoproliferative disease. Chst11-deficient mouse has severe chondrodysplasia, congenital arthritis and neonatal lethality. We searched for the causative variant for the unusual combination of limb malformations with variable expressivity accompanied by skeletal defects in a consanguineous Pakistani kindred. METHODS We performed detailed clinical investigations in family members. Homozygosity mapping using SNP genotype data was performed to map the disease locus and exome sequencing to identify the underlying molecular defect. RESULTS The limb malformations include brachydactyly, overriding digits and clino-symphalangism in hands and feet and syndactyly and hexadactyly in feet. Skeletal defects include scoliosis, dislocated patellae and fibulae and pectus excavatum. The disease locus is mapped to a 1.6 Mb region at 12q23, harbouring a homozygous in-frame deletion of 15 nucleotides in CHST11. Novel variant c.467_481del (p.L156_N160del) is deduced to lead to the deletion of five evolutionarily highly conserved amino acids and predicted as damaging to protein by in silico analysis. Our findings confirm the crucial role of CHST11 in skeletal morphogenesis and show that CHST11 defects have variable manifestations that include a variety of limb malformations and skeletal defects.
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Affiliation(s)
- Rana Muhammad Kamran Shabbir
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Gökhan Nalbant
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | - Nafees Ahmad
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Sajid Malik
- Human Genetics Program, Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
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9
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Langford R, Hurrion E, Dawson PA. Genetics and pathophysiology of mammalian sulfate biology. J Genet Genomics 2017; 44:7-20. [DOI: 10.1016/j.jgg.2016.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 12/23/2022]
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10
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Tsai EA, Shakbatyan R, Evans J, Rossetti P, Graham C, Sharma H, Lin CF, Lebo MS. Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine. J Pers Med 2016; 6:jpm6010012. [PMID: 26927186 PMCID: PMC4810391 DOI: 10.3390/jpm6010012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/27/2016] [Accepted: 02/18/2016] [Indexed: 12/20/2022] Open
Abstract
Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient’s genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally includes the sequence information of a complete genome for each individual. At Partners HealthCare Personalized Medicine, we have developed a clinical process for whole genome sequencing (WGS) with application in both healthy individuals and those with disease. In this manuscript, we will describe our bioinformatics strategy to efficiently process and deliver genomic data to geneticists for clinical interpretation. We describe the handling of data from FASTQ to the final variant list for clinical review for the final report. We will also discuss our methodology for validating this workflow and the cost implications of running WGS.
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Affiliation(s)
- Ellen A Tsai
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02138, USA.
| | - Rimma Shakbatyan
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
| | - Jason Evans
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
| | - Peter Rossetti
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
| | - Chet Graham
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
| | - Himanshu Sharma
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
| | - Chiao-Feng Lin
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02138, USA.
| | - Matthew S Lebo
- Personalized Medicine, Partners HealthCare, Cambridge, MA 02139, USA.
- Department of Pathology, Harvard Medical School, Boston, MA 02138, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
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