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Shaffer LG. Special issue on companion animal genetics: Novel variants discovered in wide variety of diseases in dogs, identification and further characterization of traits in dogs and cats, and the use of microarrays in the detection of aneuploidy in dogs. Hum Genet 2021; 140:1501-1503. [PMID: 34599369 DOI: 10.1007/s00439-021-02375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, suite 220, Spokane, WA, 99207, USA. .,Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
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Rorden C, Griswold MC, Moses N, Berry CR, Keller GG, Rivas R, Flores-Smith H, Shaffer LG, Malik R. Radiographical Survey of Osteochondrodysplasia in Scottish Fold Cats caused by the TRPV4 gene variant. Hum Genet 2021; 140:1525-1534. [PMID: 34406467 DOI: 10.1007/s00439-021-02337-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/07/2021] [Indexed: 11/26/2022]
Abstract
The unique appearance of Scottish Fold cats is caused by a single gene variant in TRPV4, which impacts the development of cartilage. This results in the ears folding forward and variable effects on articular cartilage and bone. While some find this appearance desirable, early work demonstrated that homozygous cats with two copies of this variant develop severe radiographic consequences. Subsequent breeding programs have mated heterozygous cats with straight-eared cats to ensure an equal mix of heterozygous (fold) and wild-type (nonfolded) offspring, in the hope of raising healthy cats. More recent radiological surveys suggest that these heterozygous cats may also have medical problems consisting of deformed distal extremities in the worst cases and accelerated onset of osteoarthritis. However, these previous studies were undermined by selection biases, lack of controls, unblinded assessment and lack of known genotypes. Our aim was to determine if heterozygous cats exhibit radiological abnormalities when controlling for these limitations. Specifically, DNA and radiographs were acquired for 22 Scottish Fold cats. Four reviewers, blinded to the ear phenotype, assessed the lateral radiographs. Genotyping showed that all 10 folded-ear cats were heterozygous, and none of the straight-ear cats (n = 12) had the abnormal TRPV4 variant. Although each reviewer, on average, gave a numerically worse 'severity score' to folded-ear cats relative to straight-ear cats, the images in heterozygous cats showed much milder radiological signs than previously published. This study provides additional information to be considered in the complicated debate as to whether cats with the TRPV4 variant should be bred for folded ears given the potential comorbidities.
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Affiliation(s)
- Chris Rorden
- McCausland Center for Brain Imaging and Department of Psychology, University of South Carolina, Columbia, SC, 29208, USA.
| | - Marilee C Griswold
- The Cat Fanciers' Association, Inc., Alliance, OH, 44601, USA
- Eau Claire Cooperative Health Center, Columbia, SC, 29203, USA
| | - Nan Moses
- 4 Seasons Cat Hospital, Charlotte, NC, 28226, USA
| | - Clifford R Berry
- Diagnostic Imaging, Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, 27606, USA
| | | | - Rudy Rivas
- Columbia Veterinary Emergency Trauma and Specialty, Columbia, SC, 29223, USA
| | - Helen Flores-Smith
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, 99207, USA
| | - Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, 99207, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, The University of Sydney, Sydney, Australia
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Ballif BC, Emerson LJ, Ramirez CJ, Carl CR, Sundin K, Flores-Smith H, Shaffer LG. The PMEL gene and merle (dapple) in the dachshund: cryptic, hidden, and mosaic variants demonstrate the need for genetic testing prior to breeding. Hum Genet 2021; 140:1581-1591. [PMID: 34370083 DOI: 10.1007/s00439-021-02330-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/31/2021] [Indexed: 11/26/2022]
Abstract
One of the most unique coat color patterns in the domestic dog is merle (also known as dapple in the dachshund breed), characterized by patches of normal pigmentation surrounded by diluted eumelanin pigment. In dogs, this striking variegated pattern is caused by an insertion of a SINE element into the PMEL gene. Differences in the length of the SINE insertion [due to a variable-length poly(A)-tail] has been associated with variation in the merle coat color and patterning. We previously performed a systematic evaluation of merle in 175 Australian shepherds and related breeds and correlated the length of the merle insertion variants with four broad phenotypic clusters designated as "cryptic", "atypical", "classic", and "harlequin" merle. In this study, we evaluated the SINE insertions in 140 dachshunds and identified the same major merle phenotypic clusters with only slight variation between breeds. Specifically, we identified numerous cases of true "hidden" merle in dachshunds with light/red (pheomelanin) coats with little to no black/brown pigment (eumelanin) and thus minimal or no observable merle phenotype. In addition, we identified somatic and gonadal mosaicism, with one dog having a large insertion in the harlequin size range of M281 that had no merle phenotype and unintentionally produced a double merle puppy with anophthalmia. The frequent identification of cryptic, hidden, and mosaic merle variants, which can be undetectable by phenotypic inspection, should be of particular concern to breeders and illustrates the critical need for genetic testing for merle prior to breeding to avoid producing dogs with serious health problems.
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Affiliation(s)
- Blake C Ballif
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA.
| | | | - Christina J Ramirez
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Casey R Carl
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Kyle Sundin
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Helen Flores-Smith
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA, USA
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Shaffer LG, Hopp B, Switonski M, Zahand A, Ballif BC. Identification of aneuploidy in dogs screened by a SNP microarray. Hum Genet 2021; 140:1619-1624. [PMID: 34287710 DOI: 10.1007/s00439-021-02318-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/14/2021] [Indexed: 01/23/2023]
Abstract
Microarray analysis is an efficient approach for screening and identifying cytogenetic imbalances in humans. SNP arrays, in particular, are a powerful way to identify copy-number gains and losses representing aneuploidy and aneusomy, but moreover, allow for the direct assessment of individual genotypes in known disease loci. Using these approaches, trisomies, monosomies, and mosaicism of whole chromosomes have been identified in human microarray studies. For canines, this approach is not widely used in clinical laboratory diagnostic practice. In our laboratory, we have implemented the use of a proprietary SNP array that represents approximately 650,000 loci across the domestic dog genome. During the validation of this microarray prior to clinical use, we identified three cases of aneuploidy after screening 2053 dogs of various breeds including monosomy X, trisomy X, and an apparent mosaic trisomy of canine chromosome 38 (CFA38). This study represents the first use of microarrays for copy-number evaluation to identify cytogenetic anomalies in canines. As microarray analysis becomes more routine in canine genetic testing, more cases of chromosome aneuploidy are likely to be uncovered.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc, 220 E Rowan, Suite 220, Spokane, WA, 99207, USA. .,Center for Reproductive Biology, Washington State University, Pullman, WA, USA.
| | - Bradley Hopp
- Paw Print Genetics, Genetic Veterinary Sciences, Inc, 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Marek Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Adam Zahand
- Paw Print Genetics, Genetic Veterinary Sciences, Inc, 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Blake C Ballif
- Paw Print Genetics, Genetic Veterinary Sciences, Inc, 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
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Shaffer LG. Special issue on canine genetics: animal models for human disease and gene therapies, new discoveries for canine inherited diseases, and standards and guidelines for clinical genetic testing for domestic dogs. Hum Genet 2019; 138:437-440. [PMID: 31056728 DOI: 10.1007/s00439-019-02025-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA.
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Shaffer LG, Geretschlaeger A, Ramirez CJ, Ballif BC, Carl C. Quality assurance checklist and additional considerations for canine clinical genetic testing laboratories: a follow-up to the published standards and guidelines. Hum Genet 2019; 138:501-508. [PMID: 30982136 PMCID: PMC6536464 DOI: 10.1007/s00439-019-02013-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
There is currently no oversight for canine clinical genetic testing laboratories. We published an initial set of standards and guidelines with the goal of providing a basis for which canine testing laboratories could evaluate their quality assurance programs. To further those standards and guidelines, we have developed a checklist that can be used as a self-evaluation to identify gaps in their programs for continual quality improvement over time. Because there is currently no organization willing to oversee an external proficiency program, the checklist provides the first step toward an internal, self-assessment that can be used periodically to monitor improvements. In addition, we attempt to address concerns from the canine community regarding rare or private mutations, genetic screening using array-based technologies, non-peer reviewed tests that are being offered, and the clinical validity of certain mutations in particular breeds. Through coordination, conversation and hard work, the canine genetic testing community can strive to organize to improve testing and to provide more transparency to consumers and better outcomes for dogs.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA.
| | | | - Christina J Ramirez
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Blake C Ballif
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Casey Carl
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
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Ramirez CJ, Krug M, Zahand A, Sundin K, Shaffer LG, Ballif BC. Canine factor VII deficiency: lessons learned in applying methods-based laboratory proficiency testing. J Vet Diagn Invest 2019; 31:276-279. [PMID: 30661469 DOI: 10.1177/1040638718825281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Canine inherited factor VII deficiency is a mild-to-moderate, inherited coagulopathy that affects several breeds of dog. We identified 2 polymorphisms near the disease-causing F7 gene mutation, one of which interfered with testing in several Beagles by causing allele dropout of the normal, wild-type allele. In the absence of an external proficiency program among veterinary genetic testing laboratories, implementation of an internal proficiency program, which requires 2 independent methods for genotyping dogs at any given locus, was further enhanced by ensuring minimally non-overlapping primer pairs between the 2 assays. After redesign of our clinical tests, all dogs were re-examined, and the correct genotypes were identified. These changes ensure higher accuracy in future testing of the F7 mutation.
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Affiliation(s)
| | - Melissa Krug
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Adam Zahand
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Kyle Sundin
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Lisa G Shaffer
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Blake C Ballif
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
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Ballif BC, Ramirez CJ, Carl CR, Sundin K, Krug M, Zahand A, Shaffer LG, Flores-Smith H. The PMEL Gene and Merle in the Domestic Dog: A Continuum of Insertion Lengths Leads to a Spectrum of Coat Color Variations in Australian Shepherds and Related Breeds. Cytogenet Genome Res 2018; 156:22-34. [PMID: 30071510 DOI: 10.1159/000491408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 11/19/2022] Open
Abstract
Merle is a distinct coat color and pattern found in numerous species, including the domestic dog, characterized by patches of diluted eumelanin (black pigment) interspersed among areas of normal pigmentation. In dogs, this variegated pattern is caused by an insertion of a SINE element into the canine PMEL gene. Although variation in the length of the SINE insertion - due to a variable-length poly(A) tail - has been observed to be associated with variation in merle coat color and patterning, no systematic evaluation of this correlation has been conducted and published in the scientific literature. We performed high-resolution analysis of the SINE insertion lengths in 175 dogs (99 Australian shepherds, 45 miniature Australian shepherds, and 31 miniature American shepherds) and compared the genotypes with the coat phenotypes (when available). SINE insertion lengths varied from 201 to 277 bp, indicating that merle insertion variants can occur in virtually any size along the entire continuum. Genotype-phenotype correlation of 126 dogs with only a single SINE insertion (m/M) identified at least 4 major phenotypic clusters designated as "cryptic," "atypical," "classic," and "harlequin" merle. However, we found several phenotypic outliers that did not cluster within these major groupings, suggesting that insertion size is not the only factor responsible for merle phenotypic variability. In addition, we detected 25 dogs with 2 SINE insertions (M/M) and 24 dogs with more than 2 PMEL (merle) alleles, indicating mosaicism. Genotype-phenotype correlation of M/M dogs suggests that cryptic merle alleles often act like non-merle (m) alleles when combined with atypical, classic, and harlequin-sized alleles. The finding of mosaicism has important implications for the dog's phenotype and the ability to potentially transmit various alleles to its offspring. Furthermore, we identified examples of the SINE insertion poly(A)-tail expansion and contraction between generations, which also has important implications for breeding practices and determining mating pairs to avoid producing double merle dogs. These data demonstrate that there is a continuum of merle insertion lengths associated with a spectrum of coat color and patterns and that genotype-phenotype exceptions and overlap make it difficult to strictly assign certain insertion sizes with an expected coat color, although some generalizations are possible.
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Shaffer LG, Ramirez CJ, Phelps P, Aviram M, Walczak M, Bar-Gal GK, Ballif BC. An International Genetic Survey of Breed-Specific Diseases in Working Dogs from the United States, Israel, and Poland. Cytogenet Genome Res 2018; 153:198-204. [PMID: 29421799 DOI: 10.1159/000486774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 11/19/2022] Open
Abstract
Genetic diseases occur in breeds used for law enforcement. As important team members, dogs are expected to operate at peak performance for several years and are significant investments for both the initial purchase and extensive, specialized training. Previous studies have not focused on causes for retirement or euthanasia as genetic (inherited) versus acquired (environmental). We performed direct mutational analysis for breed-specific conditions on samples from 304 dogs including 267 law enforcement (122 US, 87 Israeli, and 58 Polish) and 37 search and rescue dogs. Genetic testing identified 29% (n = 89) of the dogs tested to be carriers of a genetic mutation and 6% (n = 19) to be at risk for a debilitating inherited condition that may eventually impair the dog's ability to work. At-risk dogs included Labrador Retrievers (n = 4) with exercise-induced collapse, Bloodhounds (n = 2) with degenerative myelopathy (DM), and German Shepherd dogs with DM (n = 12) or leukocyte adhesion deficiency, type III (n = 1). A substantial number of working dogs were shown to be at risk for genetic conditions that may shorten the dog's career. The loss of dogs, due to early retirement or euthanasia, as a result of preventable genetic conditions has an emotional cost to handlers and financial cost to service organizations that can be avoided with genetic screening prior to breeding, buying, or training.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA
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Maussion G, Cruceanu C, Rosenfeld JA, Bell SC, Jollant F, Szatkiewicz J, Collins RL, Hanscom C, Kolobova I, de Champfleur NM, Blumenthal I, Chiang C, Ota V, Hultman C, O'Dushlaine C, McCarroll S, Alda M, Jacquemont S, Ordulu Z, Marshall CR, Carter MT, Shaffer LG, Sklar P, Girirajan S, Morton CC, Gusella JF, Turecki G, Stavropoulos DJ, Sullivan PF, Scherer SW, Talkowski ME, Ernst C. Cover Image, Volume 173A, Number 2, February 2017. Am J Med Genet A 2017. [DOI: 10.1002/ajmg.a.37896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gilles Maussion
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
| | - Cristiana Cruceanu
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
- Department of Human Genetics; McGill University; Montreal Canada
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories; PerkinElmer, Inc.; Spokane Washington
| | - Scott C. Bell
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
| | - Fabrice Jollant
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
- Nîmes Academic Hospital (CHU); Nîmes France
| | - Jin Szatkiewicz
- Department of Genetics; University of North Carolina; Chapel Hill North Carolina
| | - Ryan L. Collins
- Center for Human Genetic Research; Massachusetts General Hospital; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
| | - Carrie Hanscom
- Center for Human Genetic Research; Massachusetts General Hospital; Boston Massachusetts
| | - Ilaria Kolobova
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
| | | | - Ian Blumenthal
- Center for Human Genetic Research; Massachusetts General Hospital; Boston Massachusetts
| | - Colby Chiang
- Department of Biochemistry and Molecular Genetics; University of Virginia School of Medicine; Charlottesville Virginia
- McDonnell Genome Institute; Washington University School of Medicine; St. Louis Missouri
| | - Vanessa Ota
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics; Karolinska Institute; Stockholm Sweden
| | | | - Steve McCarroll
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
- Department of Genetics; Harvard Medical School; Boston Massachusetts
| | - Martin Alda
- Department of Psychiatry Halifax; Dalhousie University; Halifax Nova Scotia Canada
| | - Sebastien Jacquemont
- Department of Pediatrics; Sainte-Justine Hospital; University of Montreal; Montreal Canada
| | - Zehra Ordulu
- Department of Obstetrics, Gynecology and Reproductive Biology; Brigham and Women's Hospital; Boston Massachusetts
- Harvard Medical School; Boston Massachusetts
| | - Christian R. Marshall
- The Centre for Applied Genomics and Genetics and Genome Biology; The Hospital for Sick Children; Toronto Canada
| | - Melissa T. Carter
- Regional Genetics Program; The Children's Hospital of Eastern Ontario; Ottawa Canada
| | - Lisa G. Shaffer
- Signature Genomic Laboratories; PerkinElmer, Inc.; Spokane Washington
| | - Pamela Sklar
- Departments of Neuroscience, Psychiatry and Genetics and Genome Sciences; Mount Sinai Hospital; New York New York
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology; Pennsylvania State University; University Park; Pennsylvania
| | - Cynthia C. Morton
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
- Departments of Obstetrics, Gynecology, and Reproductive Biology and of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
- Manchester Academic Health Science Center; University of Manchester; Manchester United Kingdom
| | - James F. Gusella
- Center for Human Genetic Research; Massachusetts General Hospital; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
- Department of Genetics; Harvard Medical School; Boston Massachusetts
| | - Gustavo Turecki
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
- Department of Human Genetics; McGill University; Montreal Canada
| | - Dimitri J. Stavropoulos
- Genome Diagnostics; Department of Paediatric Laboratory Medicine; The Hospital for Sick Children; University of Toronto; Toronto Canada
| | - Patrick F. Sullivan
- Department of Genetics; University of North Carolina; Chapel Hill North Carolina
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Genetics and Genome Biology; The Hospital for Sick Children; Toronto Canada
- Department of Molecular Genetics and McLaughlin Centre; University of Toronto; Toronto Canada
| | - Michael E. Talkowski
- Center for Human Genetic Research; Massachusetts General Hospital; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
- Department of Neurology; Harvard Medical School; Boston Massachusetts
| | - Carl Ernst
- Department of Psychiatry; McGill Group for Suicide Studies, and Douglas Mental Health University Institute; Montreal Canada
- Department of Human Genetics; McGill University; Montreal Canada
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Shaffer LG, Ramirez CJ, Sundin K, Connell LB, Ballif BC. Genetic screening and mutation identification in a rare canine breed, the ceský fousek. Vet rec case rep 2017. [DOI: 10.1136/vetreccr-2016-000346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
- School of Molecular BiosciencesCollege of Veterinary MedicineWashington State UniversityPullmanWashingtonUSA
| | | | - Kyle Sundin
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
| | - Laurie B Connell
- Department of Molecular and Biomedical SciencesSchool of Marine SciencesUniversity of MaineOronoMaineUSA
| | - Blake C Ballif
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
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12
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Maussion G, Cruceanu C, Rosenfeld JA, Bell SC, Jollant F, Szatkiewicz J, Collins RL, Hanscom C, Kolobova I, de Champfleur NM, Blumenthal I, Chiang C, Ota V, Hultman C, O'Dushlaine C, McCarroll S, Alda M, Jacquemont S, Ordulu Z, Marshall CR, Carter MT, Shaffer LG, Sklar P, Girirajan S, Morton CC, Gusella JF, Turecki G, Stavropoulos DJ, Sullivan PF, Scherer SW, Talkowski ME, Ernst C. Implication of LRRC4C and DPP6 in neurodevelopmental disorders. Am J Med Genet A 2016; 173:395-406. [PMID: 27759917 DOI: 10.1002/ajmg.a.38021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/29/2016] [Indexed: 12/27/2022]
Abstract
We performed whole-genome sequencing on an individual from a family with variable psychiatric phenotypes that had a sensory processing disorder, apraxia, and autism. The proband harbored a maternally inherited balanced translocation (46,XY,t(11;14)(p12;p12)mat) that disrupted LRRC4C, a member of the highly specialized netrin G family of axon guidance molecules. The proband also inherited a paternally derived chromosomal inversion that disrupted DPP6, a potassium channel interacting protein. Copy Number (CN) analysis in 14,077 cases with neurodevelopmental disorders and 8,960 control subjects revealed that 60% of cases with exonic deletions in LRRC4C had a second clinically recognizable syndrome associated with variable clinical phenotypes, including 16p11.2, 1q44, and 2q33.1 CN syndromes, suggesting LRRC4C deletion variants may be modifiers of neurodevelopmental disorders. In vitro, functional assessments modeling patient deletions in LRRC4C suggest a negative regulatory role of these exons found in the untranslated region of LRRC4C, which has a single, terminal coding exon. These data suggest that the proband's autism may be due to the inheritance of disruptions in both DPP6 and LRRC4C, and may highlight the importance of the netrin G family and potassium channel interacting molecules in neurodevelopmental disorders. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gilles Maussion
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | - Cristiana Cruceanu
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington
| | - Scott C Bell
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | - Fabrice Jollant
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Nîmes Academic Hospital (CHU), Nîmes, France
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Ryan L Collins
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Carrie Hanscom
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Ilaria Kolobova
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | | | - Ian Blumenthal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Colby Chiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Vanessa Ota
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | | | - Steve McCarroll
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Martin Alda
- Department of Psychiatry Halifax, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sebastien Jacquemont
- Department of Pediatrics, Sainte-Justine Hospital, University of Montreal, Montreal, Canada
| | - Zehra Ordulu
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Christian R Marshall
- The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Melissa T Carter
- Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington
| | - Pamela Sklar
- Departments of Neuroscience, Psychiatry and Genetics and Genome Sciences, Mount Sinai Hospital, New York, New York
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Cynthia C Morton
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Departments of Obstetrics, Gynecology, and Reproductive Biology and of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts.,Manchester Academic Health Science Center, University of Manchester, Manchester, United Kingdom
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Stephen W Scherer
- The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Carl Ernst
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
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13
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Simons A, Shaffer LG, Hastings RJ. Cytogenetic Nomenclature: Changes in the ISCN 2013 Compared to the 2009 Edition. Cytogenet Genome Res 2015; 141:1-6. [PMID: 23817294 DOI: 10.1159/000353118] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2013] [Indexed: 11/19/2022] Open
Abstract
The latest edition of the International System for Human Cytogenetic Nomenclature, ISCN 2013, has recently been published following a thorough revision of the 2009 issue and the incorporation of suggestions from the community by the current standing committee. This review will highlight the multiple nomenclature changes in the respective chapters of the 2013 version compared to the previous version of the ISCN published in 2009. These highlights are meant as a guide for the cytogeneticist to assist in the transition in the use of this updated nomenclature for describing cytogenetic and molecular cytogenetic findings in both clinical and research reports.
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Affiliation(s)
- A Simons
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen , The Netherlands
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14
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Shaffer LG, Ramirez CJ, Sundin K, Carl C, Ballif BC. Genetic screening and mutation identification in a rare canine breed, the Drentsche patrijshond. Vet rec case rep 2015. [DOI: 10.1136/vetreccr-2015-000185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
- School of Molecular BiosciencesCollege of Veterinary MedicineWashington State UniversityPullmanWA99164USA
| | | | - Kyle Sundin
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
| | - Casey Carl
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
| | - Blake C Ballif
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
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15
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Rosenfeld JA, Fox JE, Descartes M, Brewer F, Stroud T, Gorski JL, Upton SJ, Moeschler JB, Monteleone B, Neill NJ, Lamb AN, Ballif BC, Shaffer LG, Ravnan JB. Clinical features associated with copy number variations of the 14q32 imprinted gene cluster. Am J Med Genet A 2014; 167A:345-53. [DOI: 10.1002/ajmg.a.36866] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jill A. Rosenfeld
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
| | - Joyce E. Fox
- Division of Medical Genetics; Steven and Alexandra Cohen Children's Medical Center of New York; New York
| | - Maria Descartes
- Department of Genetics; University of Alabama at Birmingham; Alabama
| | - Fallon Brewer
- Department of Genetics; University of Alabama at Birmingham; Alabama
| | - Tracy Stroud
- Division of Developmental Pediatrics; University of Missouri; Columbia Missouri
| | - Jerome L. Gorski
- Division of Medical Genetics; University of Missouri School of Medicine; Columbia Missouri
| | - Sheila J. Upton
- Children's Hospital at Dartmouth; Dartmouth-Hitchcock Medical Center; Lebanon New Hampshire
| | - John B. Moeschler
- Children's Hospital at Dartmouth; Dartmouth-Hitchcock Medical Center; Lebanon New Hampshire
| | | | - Nicholas J. Neill
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Allen N. Lamb
- ARUP Laboratories; Department of Pathology; University of Utah; Salt Lake City Utah
| | - Blake C. Ballif
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Paw Print Genetics; Genetic Veterinary Sciences; Inc.; Spokane Washington
| | - Lisa G. Shaffer
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Paw Print Genetics; Genetic Veterinary Sciences; Inc.; Spokane Washington
| | - J. Britt Ravnan
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
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16
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Midro AT, Panasiuk B, Stasiewicz-Jarocka B, Olszewska M, Wiland E, Myśliwiec M, Kurpisz M, Shaffer LG, Gajecka M. Recurrence risks for different pregnancy outcomes and meiotic segregation analysis of spermatozoa in carriers of t(1;11)(p36.22;q12.2). J Hum Genet 2014; 59:667-74. [PMID: 25319850 DOI: 10.1038/jhg.2014.92] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 01/16/2023]
Abstract
Cumulative data obtained from two relatively large pedigrees of a unique reciprocal chromosomal translocation (RCT) t(1;11)(p36.22;q12.2) ascertained by three miscarriages (pedigree 1) and the birth of newborn with hydrocephalus and myelomeningocele (pedigree 2) were used to estimate recurrence risks for different pregnancy outcomes. Submicroscopic molecular characterization by fluorescent in situ hybridization (FISH) of RCT break points in representative carriers showed similar rearrangements in both families. Meiotic segregation patterns after sperm analysis by three-color FISH of one male carrier showed all possible outcomes resulting from 2:2 and 3:1 segregations. On the basis of empirical survival data, we suggest that only one form of chromosome imbalance resulting in monosomy 1p36.22→pter with trisomy 11q12.2→qter may be observed in progeny at birth. Segregation analysis of these pedigrees was performed by the indirect method of Stengel-Rutkowski and showed that probability rate for malformed child at birth due to an unbalanced karyotype was 3/48 (6.2±3.5%) after ascertainment correction. The risk for stillbirths/early neonatal deaths was -/48 (<1.1%) and for miscarriages was 17/48 (35.4±6.9%). However, the probability rate for children with a normal phenotype at birth was 28/48 (58.3±7.1%). The results obtained from this study may be used to determine the risks for the various pregnancy outcomes for carriers of t(1;11)(p36.22;q12.2) and can be used for genetic counseling of carriers of this rearrangement.
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Affiliation(s)
- Alina Teresa Midro
- Department of Clinical Genetics, Medical University of Bialystok, Bialystok, Poland
| | - Barbara Panasiuk
- Department of Clinical Genetics, Medical University of Bialystok, Bialystok, Poland
| | | | - Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Ewa Wiland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marta Myśliwiec
- Department of Clinical Genetics, Medical University of Bialystok, Bialystok, Poland
| | - Maciej Kurpisz
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA
| | - Marzena Gajecka
- 1] Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland [2] Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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17
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Bianchi DW, Van Mieghem T, Shaffer LG, Faas BHW, Chitty LS, Ghidini A, Deprest J. In case you missed it: the Prenatal Diagnosis section editors bring you the most significant advances of 2013. Prenat Diagn 2014; 34:1-5. [PMID: 24382791 DOI: 10.1002/pd.4288] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 11/26/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Diana W Bianchi
- Mother Infant Research Institute at Tufts Medical Center, Boston, Massachusetts, USA
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18
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Cooper GM, Coe BP, Girirajan S, Rosenfeld JA, Vu TH, Baker C, Williams C, Stalker H, Hamid R, Hannig V, Abdel-Hamid H, Bader P, McCracken E, Niyazov D, Leppig K, Thiese H, Hummel M, Alexander N, Gorski J, Kussmann J, Shashi V, Johnson K, Rehder C, Ballif BC, Shaffer LG, Eichler EE. Corrigendum: A copy number variation morbidity map of developmental delay. Nat Genet 2014. [DOI: 10.1038/ng0914-1040a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Hermetz KE, Newman S, Conneely KN, Martin CL, Ballif BC, Shaffer LG, Cody JD, Rudd MK. Large inverted duplications in the human genome form via a fold-back mechanism. PLoS Genet 2014; 10:e1004139. [PMID: 24497845 PMCID: PMC3907307 DOI: 10.1371/journal.pgen.1004139] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/09/2013] [Indexed: 11/27/2022] Open
Abstract
Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes. Large duplications that include many genes can lead to both neurodevelopmental phenotypes in children and gene amplifications in tumors. There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise to the inverted dicentric chromosome in most inverted duplications remain unknown. Here we have combined high-resolution array CGH, custom sequence capture, next-generation sequencing, and long-range PCR to analyze the breakpoints of 50 nonrecurrent inverted duplications in patients with intellectual disability, autism, and congenital anomalies. For half of the rearrangements in our study, we sequenced at least one breakpoint junction. Sequence analysis of breakpoint junctions reveals a normal-copy disomic spacer between inverted and non-inverted copies of the duplication. Further, short inverted sequences are present at the boundary of the disomic spacer and the inverted duplication. These data support a mechanism of inverted duplication formation whereby a chromosome with a double-strand break intrastrand pairs with itself to form a “fold-back” intermediate that, after DNA replication, produces a dicentric inverted chromosome with a disomic spacer corresponding to the site of the fold-back loop. This process can lead to inverted duplications adjacent to terminal deletions, inverted duplications juxtaposed to translocations, and inverted duplication ring chromosomes. Chromosomes with large inverted duplications and terminal deletions cause neurodevelopmental disorders in children. These chromosome rearrangements typically involve hundreds of genes, leading to significant changes in gene dosage. Though inverted duplications adjacent to terminal deletions are a relatively common type of chromosomal imbalance, the DNA repair mechanism responsible for their formation is not known. In this study, we analyze the genomic organization of the largest collection of human inverted duplications. We find a common inverted duplication structure, consistent with a model that requires DNA to fold back and form a dicentric chromosome intermediate. These data provide insight into the formation of nonrecurrent inverted duplications in the human genome.
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Affiliation(s)
- Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Scott Newman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America ; Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, Georgia, United States of America
| | - Christa L Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Blake C Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, United States of America
| | - Jannine D Cody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America ; The Chromosome 18 Registry and Research Society, San Antonio, Texas, United States of America
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
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20
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Overhoff J, Rabideau MM, Bird LM, Schweitzer DN, Haynes K, Schultz RA, Shaffer LG, Rosenfeld JA, Ellison JW. Refinement of the 8q22.1 microdeletion critical region associated with Nablus mask-like facial syndrome. Am J Med Genet A 2013; 164A:259-63. [PMID: 24259484 DOI: 10.1002/ajmg.a.36163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 07/14/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Justin Overhoff
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington
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21
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Chowdhury S, Bandholz AM, Parkash S, Dyack S, Rideout AL, Leppig KA, Thiese H, Wheeler PG, Tsang M, Ballif BC, Shaffer LG, Torchia BS, Ellison JW, Rosenfeld JA. Phenotypic and molecular characterization of 19q12q13.1 deletions: a report of five patients. Am J Med Genet A 2013; 164A:62-9. [PMID: 24243649 DOI: 10.1002/ajmg.a.36201] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 07/25/2013] [Indexed: 12/17/2022]
Abstract
A syndrome associated with 19q13.11 microdeletions has been proposed based on seven previous cases that displayed developmental delay, intellectual disability, speech disturbances, pre- and post-natal growth retardation, microcephaly, ectodermal dysplasia, and genital malformations in males. A 324-kb critical region was previously identified as the smallest region of overlap (SRO) for this syndrome. To further characterize this microdeletion syndrome, we present five patients with deletions within 19q12q13.12 identified using a whole-genome oligonucleotide microarray. Patients 1 and 2 possess deletions overlapping the SRO, and Patients 3-5 have deletions proximal to the SRO. Patients 1 and 2 share significant phenotypic overlap with previously reported cases, providing further definition of the 19q13.11 microdeletion syndrome phenotype, including the first presentation of ectrodactyly in the syndrome. Patients 3-5, whose features include developmental delay, growth retardation, and feeding problems, support the presence of dosage-sensitive genes outside the SRO that may contribute to the abnormal phenotypes observed in this syndrome. Multiple genotype-phenotype correlations outside the SRO are explored, including further validation of the deletion of WTIP as a candidate for male hypospadias observed in this syndrome. We postulate that unique patient-specific deletions within 19q12q13.1 may explain the phenotypic variability observed in this emerging contiguous gene deletion syndrome.
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Affiliation(s)
- Shimul Chowdhury
- Providence Sacred Heart Medical Center, Molecular Diagnostics, Spokane, Washington
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22
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Abstract
The goal of prenatal cytogenetic testing is to provide reassurance to the couple seeking testing for their pregnancy, identify chromosome abnormalities in the fetus, if present, and provide treatments and medical management for affected babies. Cytogenetic analysis of banded chromosomes has been the standard for identifying chromosome abnormalities in the fetus for over 40 years. With chromosome analysis, whole chromosome aneuploidies and large structural rearrangements can be identified. The sequencing of the human genome has provided the resources to develop molecular tools that allow higher resolution observations of human chromosomes. The future holds the promise of sequencing that may identify chromosomal imbalances and deleterious single nucleotide variants. This review will focus on the use of genomic microarrays for the testing and identification of chromosome anomalies in prenatal diagnosis and will discuss the future directions of fetal testing.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA.
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23
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Carey AS, Liang L, Edwards J, Brandt T, Mei H, Sharp AJ, Hsu DT, Newburger JW, Ohye RG, Chung WK, Russell MW, Rosenfeld JA, Shaffer LG, Parides MK, Edelmann L, Gelb BD. Effect of copy number variants on outcomes for infants with single ventricle heart defects. Circ Cardiovasc Genet 2013; 6:444-51. [PMID: 24021551 PMCID: PMC3987966 DOI: 10.1161/circgenetics.113.000189] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Human genomes harbor copy number variants (CNVs), which are regions of DNA gains or losses. Although pathogenic CNVs are associated with congenital heart disease (CHD), their effect on clinical outcomes is unknown. This study sought to determine whether pathogenic CNVs among infants with single ventricle physiology were associated with inferior neurocognitive and somatic growth outcomes. METHODS AND RESULTS Genomic DNAs from 223 subjects of 2 National Heart, Lung, and Blood Institute-sponsored randomized clinical trials in infants with single ventricle CHD and 270 controls from The Cancer Genome Atlas project were analyzed for rare CNVs>300 kb using array comparative genomic hybridization. Neurocognitive and growth outcomes at 14 months from the CHD trials were compared among subjects with and without pathogenic CNVs. Putatively pathogenic CNVs, comprising 25 duplications and 6 deletions, had a prevalence of 13.9%, significantly greater than the 4.4% rate of such CNVs among controls. CNVs associated with genomic disorders were found in 13 cases but not in controls. Several CNVs likely to be causative of single ventricle CHD were observed, including aberrations altering the dosage of GATA4, MYH11, and GJA5. Subjects with pathogenic CNVs had worse linear growth, and those with CNVs associated with known genomic disorders had the poorest neurocognitive and growth outcomes. A minority of children with pathogenic CNVs were noted to be dysmorphic on clinical genetics examination. CONCLUSIONS Pathogenic CNVs seem to contribute to the cause of single ventricle forms of CHD in ≥10% of cases and are clinically subtle but adversely affect outcomes in children harboring them.
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Affiliation(s)
- Abigail S. Carey
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Li Liang
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Jonathan Edwards
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Tracy Brandt
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Hui Mei
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Andrew J. Sharp
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Daphne T. Hsu
- Pediatric Cardiology, The Children’s Hospital at Montefiore, Bronx, NY
| | | | - Richard G. Ohye
- Dept of Cardiac Surgery, Section of Pediatric Cardiovascular Surgery, University of Michigan Medical School, Ann Arbor, MI
| | - Wendy K. Chung
- Dept of Pediatrics, Columbia University Medical Center, New York, NY
| | - Mark W. Russell
- Division of Pediatric Cardiology, C.S. Mott Children’s Hospital, University of Michigan, Ann Arbor, MI
| | | | - Lisa G. Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Spokane, WA
| | - Michael K. Parides
- Dept of Health Evidence & Policy, Icahn School of Medicine at Mount Sinai, New York
| | - Lisa Edelmann
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
| | - Bruce D. Gelb
- Mindich Child Health & Development Institute, Icahn School of Medicine at Mount Sinai, New York
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York
- Dept of Pediatrics, Icahn School of Medicine at Mount Sinai, New York
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24
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Goldlust IS, Hermetz KE, Catalano LM, Barfield RT, Cozad R, Wynn G, Ozdemir AC, Conneely KN, Mulle JG, Dharamrup S, Hegde MR, Kim KH, Angle B, Colley A, Webb AE, Thorland EC, Ellison JW, Rosenfeld JA, Ballif BC, Shaffer LG, Demmer LA, Rudd MK. Mouse model implicates GNB3 duplication in a childhood obesity syndrome. Proc Natl Acad Sci U S A 2013; 110:14990-4. [PMID: 23980137 PMCID: PMC3773733 DOI: 10.1073/pnas.1305999110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Obesity is a highly heritable condition and a risk factor for other diseases, including type 2 diabetes, cardiovascular disease, hypertension, and cancer. Recently, genomic copy number variation (CNV) has been implicated in cases of early onset obesity that may be comorbid with intellectual disability. Here, we describe a recurrent CNV that causes a syndrome associated with intellectual disability, seizures, macrocephaly, and obesity. This unbalanced chromosome translocation leads to duplication of over 100 genes on chromosome 12, including the obesity candidate gene G protein β3 (GNB3). We generated a transgenic mouse model that carries an extra copy of GNB3, weighs significantly more than its wild-type littermates, and has excess intraabdominal fat accumulation. GNB3 is highly expressed in the brain, consistent with G-protein signaling involved in satiety and/or metabolism. These functional data connect GNB3 duplication and overexpression to elevated body mass index and provide evidence for a genetic syndrome caused by a recurrent CNV.
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Affiliation(s)
- Ian S. Goldlust
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Karen E. Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Lisa M. Catalano
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | | | - Rebecca Cozad
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Grace Wynn
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Alev Cagla Ozdemir
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Karen N. Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Departments of Biostatistics and Bioinformatics and
| | - Jennifer G. Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
- Epidemiology, Emory University School of Public Health, Atlanta, GA 30322
| | - Shikha Dharamrup
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Madhuri R. Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
| | - Katherine H. Kim
- Division of Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614
| | - Brad Angle
- Division of Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614
| | - Alison Colley
- Department of Clinical Genetics, South Western Sydney Local Health District, Liverpool, NSW 1871, Australia
| | - Amy E. Webb
- Amy E. Webb Pediatrics, Pismo Beach, CA 93449
| | - Erik C. Thorland
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
| | - Jay W. Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Blake C. Ballif
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Lisa G. Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207
| | - Laurie A. Demmer
- Division of Genetics and Metabolism, Tufts University School of Medicine, Boston, MA 02111; and
| | | | - M. Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322
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25
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Callaway JLA, Shaffer LG, Chitty LS, Rosenfeld JA, Crolla JA. The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature. Prenat Diagn 2013; 33:1119-23. [PMID: 23983223 PMCID: PMC4285999 DOI: 10.1002/pd.4209] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
ABSTRACT The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12 362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12 362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs. © 2013 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
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26
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Shuvarikov A, Campbell IM, Dittwald P, Neill NJ, Bialer MG, Moore C, Wheeler PG, Wallace SE, Hannibal MC, Murray MF, Giovanni MA, Terespolsky D, Sodhi S, Cassina M, Viskochil D, Moghaddam B, Herman K, Brown CW, Beck CR, Gambin A, Cheung SW, Patel A, Lamb AN, Shaffer LG, Ellison JW, Ravnan JB, Stankiewicz P, Rosenfeld JA. Recurrent HERV-H-mediated 3q13.2-q13.31 deletions cause a syndrome of hypotonia and motor, language, and cognitive delays. Hum Mutat 2013; 34:1415-23. [PMID: 23878096 DOI: 10.1002/humu.22384] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/11/2013] [Indexed: 11/09/2022]
Abstract
We describe the molecular and clinical characterization of nine individuals with recurrent, 3.4-Mb, de novo deletions of 3q13.2-q13.31 detected by chromosomal microarray analysis. All individuals have hypotonia and language and motor delays; they variably express mild to moderate cognitive delays (8/9), abnormal behavior (7/9), and autism spectrum disorders (3/9). Common facial features include downslanting palpebral fissures with epicanthal folds, a slightly bulbous nose, and relative macrocephaly. Twenty-eight genes map to the deleted region, including four strong candidate genes, DRD3, ZBTB20, GAP43, and BOC, with important roles in neural and/or muscular development. Analysis of the breakpoint regions based on array data revealed directly oriented human endogenous retrovirus (HERV-H) elements of ~5 kb in size and of >95% DNA sequence identity flanking the deletion. Subsequent DNA sequencing revealed different deletion breakpoints and suggested nonallelic homologous recombination (NAHR) between HERV-H elements as a mechanism of deletion formation, analogous to HERV-I-flanked and NAHR-mediated AZFa deletions. We propose that similar HERV elements may also mediate other recurrent deletion and duplication events on a genome-wide scale. Observation of rare recurrent chromosomal events such as these deletions helps to further the understanding of mechanisms behind naturally occurring variation in the human genome and its contribution to genetic disease.
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Affiliation(s)
- Andrey Shuvarikov
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, Washington
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Shiba N, Daza RAM, Shaffer LG, Barkovich AJ, Dobyns WB, Hevner RF. Neuropathology of brain and spinal malformations in a case of monosomy 1p36. Acta Neuropathol Commun 2013; 1:45. [PMID: 24252393 PMCID: PMC3893467 DOI: 10.1186/2051-5960-1-45] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 07/18/2013] [Indexed: 11/10/2022] Open
Abstract
Monosomy 1p36 is the most common subtelomeric chromosomal deletion linked to mental retardation and seizures. Neuroimaging studies suggest that monosomy 1p36 is associated with brain malformations including polymicrogyria and nodular heterotopia, but the histopathology of these lesions is unknown. Here we present postmortem neuropathological findings from a 10 year-old girl with monosomy 1p36, who died of respiratory complications. The findings included micrencephaly, periventricular nodular heterotopia in occipitotemporal lobes, cortical dysgenesis resembling polymicrogyria in dorsolateral frontal lobes, hippocampal malrotation, callosal hypoplasia, superiorly rotated cerebellum with small vermis, and lumbosacral hydromyelia. The abnormal cortex exhibited “festooned” (undulating) supragranular layers, but no significant fusion of the molecular layer. Deletion mapping demonstrated single copy loss of a contiguous 1p36 terminal region encompassing many important neurodevelopmental genes, among them four HES genes implicated in regulating neural stem cell differentiation, and TP73, a monoallelically expressed gene. Our results suggest that brain and spinal malformations in monosomy 1p36 may be more extensive than previously recognized, and may depend on the parental origin of deleted genes. More broadly, our results suggest that specific genetic disorders may cause distinct forms of cortical dysgenesis.
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Bianchi DW, Chitty LS, Deprest J, Ghidini A, Shaffer LG, Cousens RKJ. The 2012 Malcolm Ferguson-Smith Young Investigator Award. Prenat Diagn 2013; 33:619-20. [DOI: 10.1002/pd.4169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Lyn S. Chitty
- University College London NHS Foundation Trust; London UK
| | - Jan Deprest
- University Hospital Gasthuisberg; Leuven Belgium
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Repnikova EA, Rosenfeld JA, Bailes A, Weber C, Erdman L, McKinney A, Ramsey S, Hashimoto S, Lamb Thrush D, Astbury C, Reshmi SC, Shaffer LG, Gastier-Foster JM, Pyatt RE. Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization. Forensic Sci Int Genet 2013; 7:475-81. [PMID: 23948316 DOI: 10.1016/j.fsigen.2013.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 05/07/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022]
Abstract
Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci.
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Affiliation(s)
- Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
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30
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Curry CJ, Rosenfeld JA, Grant E, Gripp KW, Anderson C, Aylsworth AS, Saad TB, Chizhikov VV, Dybose G, Fagerberg C, Falco M, Fels C, Fichera M, Graakjaer J, Greco D, Hair J, Hopkins E, Huggins M, Ladda R, Li C, Moeschler J, Nowaczyk MJM, Ozmore JR, Reitano S, Romano C, Roos L, Schnur RE, Sell S, Suwannarat P, Svaneby D, Szybowska M, Tarnopolsky M, Tervo R, Tsai ACH, Tucker M, Vallee S, Wheeler FC, Zand DJ, Barkovich AJ, Aradhya S, Shaffer LG, Dobyns WB. The duplication 17p13.3 phenotype: analysis of 21 families delineates developmental, behavioral and brain abnormalities, and rare variant phenotypes. Am J Med Genet A 2013; 161A:1833-52. [PMID: 23813913 DOI: 10.1002/ajmg.a.35996] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 03/31/2013] [Indexed: 11/11/2022]
Abstract
Chromosome 17p13.3 is a gene rich region that when deleted is associated with the well-known Miller-Dieker syndrome. A recently described duplication syndrome involving this region has been associated with intellectual impairment, autism and occasional brain MRI abnormalities. We report 34 additional patients from 21 families to further delineate the clinical, neurological, behavioral, and brain imaging findings. We found a highly diverse phenotype with inter- and intrafamilial variability, especially in cognitive development. The most specific phenotype occurred in individuals with large duplications that include both the YWHAE and LIS1 genes. These patients had a relatively distinct facial phenotype and frequent structural brain abnormalities involving the corpus callosum, cerebellar vermis, and cranial base. Autism spectrum disorders were seen in a third of duplication probands, most commonly in those with duplications of YWHAE and flanking genes such as CRK. The typical neurobehavioral phenotype was usually seen in those with the larger duplications. We did not confirm the association of early overgrowth with involvement of YWHAE and CRK, or growth failure with duplications of LIS1. Older patients were often overweight. Three variant phenotypes included cleft lip/palate (CLP), split hand/foot with long bone deficiency (SHFLD), and a connective tissue phenotype resembling Marfan syndrome. The duplications in patients with clefts appear to disrupt ABR, while the SHFLD phenotype was associated with duplication of BHLHA9 as noted in two recent reports. The connective tissue phenotype did not have a convincing critical region. Our experience with this large cohort expands knowledge of this diverse duplication syndrome.
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Mullegama SV, Rosenfeld JA, Orellana C, van Bon BWM, Halbach S, Repnikova EA, Brick L, Li C, Dupuis L, Rosello M, Aradhya S, Stavropoulos DJ, Manickam K, Mitchell E, Hodge JC, Talkowski ME, Gusella JF, Keller K, Zonana J, Schwartz S, Pyatt RE, Waggoner DJ, Shaffer LG, Lin AE, de Vries BBA, Mendoza-Londono R, Elsea SH. Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder. Eur J Hum Genet 2013; 22:57-63. [PMID: 23632792 DOI: 10.1038/ejhg.2013.67] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/26/2013] [Accepted: 02/14/2013] [Indexed: 02/06/2023] Open
Abstract
Copy number variations associated with abnormal gene dosage have an important role in the genetic etiology of many neurodevelopmental disorders, including intellectual disability (ID) and autism. We hypothesize that the chromosome 2q23.1 region encompassing MBD5 is a dosage-dependent region, wherein deletion or duplication results in altered gene dosage. We previously established the 2q23.1 microdeletion syndrome and report herein 23 individuals with 2q23.1 duplications, thus establishing a complementary duplication syndrome. The observed phenotype includes ID, language impairments, infantile hypotonia and gross motor delay, behavioral problems, autistic features, dysmorphic facial features (pinnae anomalies, arched eyebrows, prominent nose, small chin, thin upper lip), and minor digital anomalies (fifth finger clinodactyly and large broad first toe). The microduplication size varies among all cases and ranges from 68 kb to 53.7 Mb, encompassing a region that includes MBD5, an important factor in methylation patterning and epigenetic regulation. We previously reported that haploinsufficiency of MBD5 is the primary causal factor in 2q23.1 microdeletion syndrome and that mutations in MBD5 are associated with autism. In this study, we demonstrate that MBD5 is the only gene in common among all duplication cases and that overexpression of MBD5 is likely responsible for the core clinical features present in 2q23.1 microduplication syndrome. Phenotypic analyses suggest that 2q23.1 duplication results in a slightly less severe phenotype than the reciprocal deletion. The features associated with a deletion, mutation or duplication of MBD5 and the gene expression changes observed support MBD5 as a dosage-sensitive gene critical for normal development.
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Affiliation(s)
- Sureni V Mullegama
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA
| | - Carmen Orellana
- Service of Genetics and Prenatal Diagnosis, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Sara Halbach
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Lauren Brick
- Department of Pediatrics, Clinical Genetics Program, McMaster University Medical Center and McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Chumei Li
- Department of Pediatrics, Clinical Genetics Program, McMaster University Medical Center and McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Lucie Dupuis
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Monica Rosello
- Service of Genetics and Prenatal Diagnosis, University and Polytechnic Hospital La Fe, Valencia, Spain
| | | | - D James Stavropoulos
- 1] Cytogenetics Laboratory, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada [2] Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
| | | | - Elyse Mitchell
- 1] Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA [2] Department of Medical Genetics, Mayo Clinic, Rochester, MN, USA
| | - Jennelle C Hodge
- 1] Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA [2] Department of Medical Genetics, Mayo Clinic, Rochester, MN, USA
| | - Michael E Talkowski
- 1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA [2] Program in Medical and Population Genetics, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA [3] Departments of Genetics and Neurology, Harvard Medical School, Cambridge, MA, USA
| | - James F Gusella
- 1] Program in Medical and Population Genetics, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA [2] Departments of Genetics and Neurology, Harvard Medical School, Cambridge, MA, USA [3] Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - Kory Keller
- Department of Molecular and Medical Genetics, Child Development and Rehabilitation Center, Oregon Health and Science University, Portland, OR, USA
| | - Jonathan Zonana
- Department of Molecular and Medical Genetics, Child Development and Rehabilitation Center, Oregon Health and Science University, Portland, OR, USA
| | - Stuart Schwartz
- Laboratory Corporation of America, Research Triangle Park, Durham, NC, USA
| | - Robert E Pyatt
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Darrel J Waggoner
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA
| | - Angela E Lin
- 1] Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA [2] Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Roberto Mendoza-Londono
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Sarah H Elsea
- 1] Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA [2] Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA [3] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Shaffer LG, Ballif BC, Theisen A, Rorem E, Bejjani BA, Torchia BA. In the middle of it all: a centered approach to chromosome analysis. ACTA ACUST UNITED AC 2013; 2:221-9. [PMID: 23485141 DOI: 10.1517/17530059.2.2.221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND The pericentromeric areas immediately flanking the centromeres are prone to instability owing to their high levels of repetitive sequences. This genomic instability makes the pericentromeric regions ideal candidates for the investigation of chromosomal abnormalities resulting in genetic disease. However, it is this instability that confounds attempts to analyze these regions of the genome. The sequencing of the human genome, while illuminating the complexity of the pericentromeric regions, has enabled the development of high-resolution microarrays for the characterization of chromosomal abnormalities. OBJECTIVE The MarkerChip(™) was developed specifically to target the pericentromeres for the identification and characterization of pericentromeric chromosomal abnormalities. METHODS The authors' experience with this microarray is reviewed in their clinical diagnostic laboratory. RESULTS/DISCUSSION The MarkerChip demonstrates the utility of constructing a microarray for the analysis of chromosome abnormalities with coverage concentrated on areas of the genome particularly susceptible to rearrangement.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, 120 N Pine St, Spokane, WA 99202, USA +1 509 474 6840 ; +1 509 474 6839 ;
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33
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Dabell MP, Rosenfeld JA, Bader P, Escobar LF, El-Khechen D, Vallee SE, Dinulos MBP, Curry C, Fisher J, Tervo R, Hannibal MC, Siefkas K, Wyatt PR, Hughes L, Smith R, Ellingwood S, Lacassie Y, Stroud T, Farrell SA, Sanchez-Lara PA, Randolph LM, Niyazov D, Stevens CA, Schoonveld C, Skidmore D, MacKay S, Miles JH, Moodley M, Huillet A, Neill NJ, Ellison JW, Ballif BC, Shaffer LG. Investigation ofNRXN1deletions: Clinical and molecular characterization. Am J Med Genet A 2013; 161A:717-31. [DOI: 10.1002/ajmg.a.35780] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/29/2012] [Indexed: 01/01/2023]
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Ernst C, Marshall CR, Shen Y, Metcalfe K, Rosenfeld J, Hodge JC, Torres A, Blumenthal I, Chiang C, Pillalamarri V, Crapper L, Diallo AB, Ruderfer D, Pereira S, Sklar P, Purcell S, Wildin RS, Spencer AC, Quade BF, Harris DJ, Lemyre E, Wu BL, Stavropoulos DJ, Geraghty MT, Shaffer LG, Morton CC, Scherer SW, Gusella JF, Talkowski ME. Highly penetrant alterations of a critical region including BDNF in human psychopathology and obesity. ACTA ACUST UNITED AC 2013; 69:1238-46. [PMID: 23044507 DOI: 10.1001/archgenpsychiatry.2012.660] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT Brain-derived neurotrophic factor (BDNF) is suspected of being a causative factor in psychiatric disorders based on case reports or studies involving large structural anomalies. OBJECTIVE To determine the involvement of BDNF in human psychopathology. DESIGN Case-control study. SETTING Microarray-based comparative genomic hybridization data from 7 molecular diagnostic centers including 38 550 affected subjects and 28 705 unaffected subjects. PATIENTS Subjects referred to diagnostic screening centers for microarray-based comparative genomic hybridization for physical or cognitive impairment. MAIN OUTCOME MEASURES Genomic copy number gains and losses. RESULTS We report 5 individuals with psychopathology and genomic deletion of a critical region including BDNF. The defined critical region was never disrupted in control subjects or diagnostic cases without developmental abnormalities. CONCLUSION Hemizygosity of the BDNF region contributes to variable psychiatric phenotypes including anxiety, behavioral, and mood disorders.
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Nguyen LS, Kim HG, Rosenfeld JA, Shen Y, Gusella JF, Lacassie Y, Layman LC, Shaffer LG, Gécz J. Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders. Hum Mol Genet 2013; 22:1816-25. [PMID: 23376982 DOI: 10.1093/hmg/ddt035] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway functions not only to degrade transcripts containing premature termination codons (PTC), but also to regulate the transcriptome. UPF3B and RBM8A, important components of NMD, have been implicated in various forms of intellectual disability (ID) and Thrombocytopenia with Absent Radius (TAR) syndrome, which is also associated with ID. To gauge the contribution of other NMD factors to ID, we performed a comprehensive search for copy number variants (CNVs) of 18 NMD genes among individuals with ID and/or congenital anomalies. We identified 11 cases with heterozygous deletions of the genomic region encompassing UPF2, which encodes for a direct interacting protein of UPF3B. Using RNA-Seq, we showed that the genome-wide consequence of reduced expression of UPF2 is similar to that seen in patients with UPF3B mutations. Out of the 1009 genes found deregulated in patients with UPF2 deletions by at least 2-fold, majority (95%) were deregulated similarly in patients with UPF3B mutations. This supports the major role of deletion of UPF2 in ID. Furthermore, we found that four other NMD genes, UPF3A, SMG6, EIF4A3 and RNPS1 are frequently deleted and/or duplicated in the patients. We postulate that dosage imbalances of these NMD genes are likely to be the causes or act as predisposing factors for neuro-developmental disorders. Our findings further emphasize the importance of NMD pathway(s) in learning and memory.
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Affiliation(s)
- Lam S Nguyen
- School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, SA 5006, Australia
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36
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Lindgren AM, Hoyos T, Talkowski ME, Hanscom C, Blumenthal I, Chiang C, Ernst C, Pereira S, Ordulu Z, Clericuzio C, Drautz JM, Rosenfeld JA, Shaffer LG, Velsher L, Pynn T, Vermeesch J, Harris DJ, Gusella JF, Liao EC, Morton CC. Haploinsufficiency of KDM6A is associated with severe psychomotor retardation, global growth restriction, seizures and cleft palate. Hum Genet 2013; 132:537-52. [PMID: 23354975 DOI: 10.1007/s00439-013-1263-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 01/02/2013] [Indexed: 12/17/2022]
Abstract
We describe a female subject (DGAP100) with a 46,X,t(X;5)(p11.3;q35.3)inv(5)(q35.3q35.1)dn, severe psychomotor retardation with hypotonia, global postnatal growth restriction, microcephaly, globally reduced cerebral volume, seizures, facial dysmorphia and cleft palate. Fluorescence in situ hybridization and whole-genome sequencing demonstrated that the X chromosome breakpoint disrupts KDM6A in the second intron. No genes were directly disrupted on chromosome 5. KDM6A is a histone 3 lysine 27 demethylase and a histone 3 lysine 4 methyltransferase. Expression of KDM6A is significantly reduced in DGAP100 lymphoblastoid cells compared to control samples. We identified nine additional cases with neurodevelopmental delay and various other features consistent with the DGAP100 phenotype with copy number variation encompassing KDM6A from microarray databases. We evaluated haploinsufficiency of kdm6a in a zebrafish model. kdm6a is expressed in the pharyngeal arches and ethmoid plate of the developing zebrafish, while a kdm6a morpholino knockdown exhibited craniofacial defects. We conclude KDM6A dosage regulation is associated with severe and diverse structural defects and developmental abnormalities.
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Affiliation(s)
- Amelia M Lindgren
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, USA
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Handrigan GR, Chitayat D, Lionel AC, Pinsk M, Vaags AK, Marshall CR, Dyack S, Escobar LF, Fernandez BA, Stegman JC, Rosenfeld JA, Shaffer LG, Goodenberger M, Hodge JC, Cain JE, Babul-Hirji R, Stavropoulos DJ, Yiu V, Scherer SW, Rosenblum ND. Deletions in 16q24.2 are associated with autism spectrum disorder, intellectual disability and congenital renal malformation. J Med Genet 2013; 50:163-73. [DOI: 10.1136/jmedgenet-2012-101288] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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38
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Rosenfeld JA, Kim KH, Angle B, Troxell R, Gorski JL, Westemeyer M, Frydman M, Senturias Y, Earl D, Torchia B, Schultz RA, Ellison JW, Tsuchiya K, Zimmerman S, Smolarek TA, Ballif BC, Shaffer LG. Further Evidence of Contrasting Phenotypes Caused by Reciprocal Deletions and Duplications: Duplication of NSD1 Causes Growth Retardation and Microcephaly. Mol Syndromol 2013; 3:247-54. [PMID: 23599694 DOI: 10.1159/000345578] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/29/2012] [Indexed: 12/15/2022] Open
Abstract
Microduplications of the Sotos syndrome region containing NSD1 on 5q35 have recently been proposed to cause a syndrome of microcephaly, short stature and developmental delay. To further characterize this emerging syndrome, we report the clinical details of 12 individuals from 8 families found to have interstitial duplications involving NSD1, ranging in size from 370 kb to 3.7 Mb. All individuals are microcephalic, and height and childhood weight range from below average to severely restricted. Mild-to-moderate learning disabilities and/or developmental delay are present in all individuals, including carrier family members of probands; dysmorphic features and digital anomalies are present in a majority. Craniosynostosis is present in the individual with the largest duplication, though the duplication does not include MSX2, mutations of which can cause craniosynostosis, on 5q35.2. A comparison of the smallest duplication in our cohort that includes the entire NSD1 gene to the individual with the largest duplication that only partially overlaps NSD1 suggests that whole-gene duplication of NSD1 in and of itself may be sufficient to cause the abnormal growth parameters seen in these patients. NSD1 duplications may therefore be added to a growing list of copy number variations for which deletion and duplication of specific genes have contrasting effects on body development.
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Affiliation(s)
- J A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Wash., USA
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Schultz RA, Tsuchiya K, Furrow A, Slovak ML, McDaniel LD, Wall M, Crawford E, Ning Y, Saleki R, Fang M, Cawich V, Johnson CE, Minier SL, Neill NJ, Morton SA, Byerly S, Surti U, Brown TC, Ballif BC, Shaffer LG. CGH-based microarray detection of cryptic and novel copy number alterations and balanced translocations in cytogenetically abnormal cases of b-cell all. Health (London) 2013. [DOI: 10.4236/health.2013.55a004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Various microarray platforms, including BAC, oligonucleotide, and SNP arrays, have been shown to -provide clinically useful diagnostic and prognostic information for patients with myelodysplastic syndromes (MDS). Clinically useful arrays are designed with specific purposes in mind and with attention to genomic content and probe density. All array types have been shown to detect genomic copy gains and losses, with SNP arrays having the added advantage of detecting copy neutral loss of heterozygosity (CNLOH). The finding of CNLOH has led to the identification of certain disease genes implicated in the initiation or progression of myeloid diseases. In addition, SNP karyotyping alone, or in conjunction with routine cytogenetics, can affect the outcome prediction and improve prognostic stratification of patients with MDS. Patients who were reclassified after array testing as having adverse-risk chromosomal findings correlated with poor survival. Results of over 25 published studies support the use of arrays in MDS testing. Because few balanced translocations are found in MDS, this disease is particularly amenable to microarray testing, and studies have shown better disease classification, identification of cryptic changes, and prognostication in this heterogeneous group of disorders. Novel genomic alterations identified by array testing may lead to better targeted therapies for treating patients with MDS.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA.
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41
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Talkowski ME, Maussion G, Crapper L, Rosenfeld JA, Blumenthal I, Hanscom C, Chiang C, Lindgren A, Pereira S, Ruderfer D, Diallo AB, Lopez JP, Turecki G, Chen ES, Gigek C, Harris DJ, Lip V, An Y, Biagioli M, Macdonald ME, Lin M, Haggarty SJ, Sklar P, Purcell S, Kellis M, Schwartz S, Shaffer LG, Natowicz MR, Shen Y, Morton CC, Gusella JF, Ernst C. Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities. Am J Hum Genet 2012; 91:1128-34. [PMID: 23217328 DOI: 10.1016/j.ajhg.2012.10.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 10/09/2012] [Accepted: 10/19/2012] [Indexed: 12/27/2022] Open
Abstract
Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA product is expressed in all tissues measured, but most abundantly in brain. Among a series of additional, unrelated subjects referred for clinical diagnostic testing who showed CNV affecting this locus, we identified four with exon-crossing deletions in association with neurodevelopmental abnormalities. No disruption of the LINC00299 coding sequence was seen in almost 14,000 control subjects. Together, these subjects with disruption of LINC00299 implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders.
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Affiliation(s)
- Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
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42
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Wapner RJ, Martin CL, Levy B, Ballif BC, Eng CM, Zachary JM, Savage M, Platt LD, Saltzman D, Grobman WA, Klugman S, Scholl T, Simpson JL, McCall K, Aggarwal VS, Bunke B, Nahum O, Patel A, Lamb AN, Thom EA, Beaudet AL, Ledbetter DH, Shaffer LG, Jackson L. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med 2012; 367:2175-84. [PMID: 23215555 PMCID: PMC3549418 DOI: 10.1056/nejmoa1203382] [Citation(s) in RCA: 862] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND Chromosomal microarray analysis has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. We aimed to evaluate the accuracy, efficacy, and incremental yield of chromosomal microarray analysis as compared with karyotyping for routine prenatal diagnosis. METHODS Samples from women undergoing prenatal diagnosis at 29 centers were sent to a central karyotyping laboratory. Each sample was split in two; standard karyotyping was performed on one portion and the other was sent to one of four laboratories for chromosomal microarray. RESULTS We enrolled a total of 4406 women. Indications for prenatal diagnosis were advanced maternal age (46.6%), abnormal result on Down's syndrome screening (18.8%), structural anomalies on ultrasonography (25.2%), and other indications (9.4%). In 4340 (98.8%) of the fetal samples, microarray analysis was successful; 87.9% of samples could be used without tissue culture. Microarray analysis of the 4282 nonmosaic samples identified all the aneuploidies and unbalanced rearrangements identified on karyotyping but did not identify balanced translocations and fetal triploidy. In samples with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 6.0% with a structural anomaly and in 1.7% of those whose indications were advanced maternal age or positive screening results. CONCLUSIONS In the context of prenatal diagnostic testing, chromosomal microarray analysis identified additional, clinically significant cytogenetic information as compared with karyotyping and was equally efficacious in identifying aneuploidies and unbalanced rearrangements but did not identify balanced translocations and triploidies. (Funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and others; ClinicalTrials.gov number, NCT01279733.).
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Affiliation(s)
- Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA.
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43
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Talkowski ME, Ordulu Z, Pillalamarri V, Benson CB, Blumenthal I, Connolly S, Hanscom C, Hussain N, Pereira S, Picker J, Rosenfeld JA, Shaffer LG, Wilkins-Haug LE, Gusella JF, Morton CC. Clinical diagnosis by whole-genome sequencing of a prenatal sample. N Engl J Med 2012; 367:2226-32. [PMID: 23215558 PMCID: PMC3579222 DOI: 10.1056/nejmoa1208594] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conventional cytogenetic testing offers low-resolution detection of balanced karyotypic abnormalities but cannot provide the precise, gene-level knowledge required to predict outcomes. The use of high-resolution whole-genome deep sequencing is currently impractical for the purpose of routine clinical care. We show here that whole-genome "jumping libraries" can offer an immediately applicable, nucleotide-level complement to conventional genetic diagnostics within a time frame that allows for clinical action. We performed large-insert sequencing of DNA extracted from amniotic-fluid cells with a balanced de novo translocation. The amniotic-fluid sample was from a patient in the third trimester of pregnancy who underwent amniocentesis because of severe polyhydramnios after multiple fetal anomalies had been detected on ultrasonography. Using a 13-day sequence and analysis pipeline, we discovered direct disruption of CHD7, a causal locus in the CHARGE syndrome (coloboma of the eye, heart anomaly, atresia of the choanae, retardation, and genital and ear anomalies). Clinical findings at birth were consistent with the CHARGE syndrome, a diagnosis that could not have been reliably inferred from the cytogenetic breakpoint. This case study illustrates the potential power of customized whole-genome jumping libraries when used to augment prenatal karyotyping.
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Affiliation(s)
- Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
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44
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Ellison JW, Ravnan JB, Rosenfeld JA, Morton SA, Neill NJ, Williams MS, Lewis J, Torchia BS, Walker C, Traylor RN, Moles K, Miller E, Lantz J, Valentin C, Minier SL, Leiser K, Powell BR, Wilks TM, Shaffer LG. Clinical utility of chromosomal microarray analysis. Pediatrics 2012; 130:e1085-95. [PMID: 23071206 DOI: 10.1542/peds.2012-0568] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To test the hypothesis that chromosomal microarray analysis frequently diagnoses conditions that require specific medical follow-up and that referring physicians respond appropriately to abnormal test results. METHODS A total of 46,298 postnatal patients were tested by chromosomal microarray analysis for a variety of indications, most commonly intellectual disability/developmental delay, congenital anomalies, dysmorphic features, and neurobehavioral problems. The frequency of detection of abnormalities associated with actionable clinical features was tallied, and the rate of physician response to a subset of abnormal tests results was monitored. RESULTS A total of 2088 diagnoses were made of more than 100 different disorders that have specific clinical features that warrant follow-up. The detection rate for these conditions using high-resolution whole-genome microarrays was 5.4%, which translates to 35% of all clinically significant abnormal test results identified in our laboratory. In a subset of cases monitored for physician response, appropriate clinical action was taken more than 90% of the time as a direct result of the microarray finding. CONCLUSIONS The disorders diagnosed by chromosomal microarray analysis frequently have clinical features that need medical attention, and physicians respond to the diagnoses with specific clinical actions, thus arguing that microarray testing provides clinical utility for a significant number of patients tested.
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Affiliation(s)
- Jay W Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, Washington 99207, USA.
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45
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Girirajan S, Rosenfeld JA, Coe BP, Parikh S, Friedman N, Goldstein A, Filipink RA, McConnell JS, Angle B, Meschino WS, Nezarati MM, Asamoah A, Jackson KE, Gowans GC, Martin JA, Carmany EP, Stockton DW, Schnur RE, Penney LS, Martin DM, Raskin S, Leppig K, Thiese H, Smith R, Aberg E, Niyazov DM, Escobar LF, El-Khechen D, Johnson KD, Lebel RR, Siefkas K, Ball S, Shur N, McGuire M, Brasington CK, Spence JE, Martin LS, Clericuzio C, Ballif BC, Shaffer LG, Eichler EE. Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med 2012; 367:1321-31. [PMID: 22970919 PMCID: PMC3494411 DOI: 10.1056/nejmoa1200395] [Citation(s) in RCA: 412] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Some copy-number variants are associated with genomic disorders with extreme phenotypic heterogeneity. The cause of this variation is unknown, which presents challenges in genetic diagnosis, counseling, and management. METHODS We analyzed the genomes of 2312 children known to carry a copy-number variant associated with intellectual disability and congenital abnormalities, using array comparative genomic hybridization. RESULTS Among the affected children, 10.1% carried a second large copy-number variant in addition to the primary genetic lesion. We identified seven genomic disorders, each defined by a specific copy-number variant, in which the affected children were more likely to carry multiple copy-number variants than were controls. We found that syndromic disorders could be distinguished from those with extreme phenotypic heterogeneity on the basis of the total number of copy-number variants and whether the variants are inherited or de novo. Children who carried two large copy-number variants of unknown clinical significance were eight times as likely to have developmental delay as were controls (odds ratio, 8.16; 95% confidence interval, 5.33 to 13.07; P=2.11×10(-38)). Among affected children, inherited copy-number variants tended to co-occur with a second-site large copy-number variant (Spearman correlation coefficient, 0.66; P<0.001). Boys were more likely than girls to have disorders of phenotypic heterogeneity (P<0.001), and mothers were more likely than fathers to transmit second-site copy-number variants to their offspring (P=0.02). CONCLUSIONS Multiple, large copy-number variants, including those of unknown pathogenic significance, compound to result in a severe clinical presentation, and secondary copy-number variants are preferentially transmitted from maternal carriers. (Funded by the Simons Foundation Autism Research Initiative and the National Institutes of Health.).
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Affiliation(s)
- Santhosh Girirajan
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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46
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Shaffer LG, Rosenfeld JA, Dabell MP, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Fisher AJ. Detection rates of clinically significant genomic alterations by microarray analysis for specific anomalies detected by ultrasound. Prenat Diagn 2012; 32:986-95. [PMID: 22847778 PMCID: PMC3509216 DOI: 10.1002/pd.3943] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/01/2012] [Accepted: 06/26/2012] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study is to understand the diagnostic utility of comparative genomic hybridization (CGH)-based microarrays for pregnancies with abnormal ultrasound findings. METHODS We performed a retrospective analysis of 2858 pregnancies with abnormal ultrasounds and normal karyotypes (when performed) tested in our laboratory using CGH microarrays targeted to known chromosomal syndromes with later versions providing backbone coverage of the entire genome. Abnormalities were stratified according to organ system involvement. Detection rates for clinically significant findings among these categories were calculated. RESULTS Clinically significant genomic alterations were identified in cases with a single ultrasound anomaly (n = 99/1773, 5.6%), anomalies in two or more organ systems (n = 77/808, 9.5%), isolated growth abnormalities (n = 2/76, 2.6%), and soft markers (n = 2/77, 2.6%). The following anomalies in isolation or with additional anomalies had particularly high detection rates: holoprosencephaly (n = 9/85, 10.6%), posterior fossa defects (n = 21/144, 14.6%), skeletal anomalies (n = 15/140, 10.7%), ventricular septal defect (n = 14/132, 10.6%), hypoplastic left heart (n = 11/68, 16.2%), and cleft lip/palate (n = 14/136, 10.3%). CONCLUSIONS Microarray analysis identified clinically significant genomic alterations in 6.5% of cases with one or more abnormal ultrasound findings; the majority were below the resolution of karyotyping. Larger data sets such as this allow for sub-stratification by specific anomalies to determine risks for genomic alterations detectable by microarray analysis.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, USA.
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Abstract
In the past decade, we have witnessed a flood of reports about mutations that cause or contribute to intellectual disability (ID). This rapid progress has been driven in large part by the implementation of chromosomal microarray analysis and next-generation sequencing methods. The findings have revealed extensive genetic heterogeneity for ID, as well as examples of a common genetic etiology for ID and other neurobehavioral/psychiatric phenotypes. Clinical diagnostic application of these new findings is already well under way, despite incomplete understanding of non-Mendelian transmission patterns that are sometimes observed.
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Affiliation(s)
- Jay W Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington 99207, USA.
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Shaffer LG, Dabell MP, Rosenfeld JA, Neill NJ, Ballif BC, Coppinger J, Diwan NR, Chong K, Shohat M, Chitayat D. Referral patterns for microarray testing in prenatal diagnosis. Prenat Diagn 2012; 32:344-50. [PMID: 22467165 DOI: 10.1002/pd.3856] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To understand the prenatal referral patterns from the United States, Canada, and Israel for two whole-genome microarray platforms, each with a different resolution. METHOD Physicians selected one of the two array designs to be performed on 1483 prenatal specimens for a 1-year period. We retrospectively examined detection rates, indications for study, and physician array selection. RESULTS The lower resolution array (55 K) showed an ~32% decrease in the detection of results of unclear clinical significance while retaining the ability to detect all but one significant abnormality identified by the higher resolution array (135 K). A majority of samples were referred for abnormal ultrasound findings. Whereas the United States and Canada utilized the higher resolution array more often for this indication, Israel preferred the 55 K array. Referral patterns for parental anxiety were similar for the United States and Israel, with most cases being tested on the 55 K array. Few cases were referred for advanced maternal age or family history of a genetic condition from either Canada or Israel. CONCLUSION Referral patterns varied between the countries and between indications for study. Understanding these differences will provide laboratories the critical information needed to develop array designs to meet the medical needs and patient desires for prenatal testing.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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49
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Traylor RN, Dobyns WB, Rosenfeld JA, Wheeler P, Spence JE, Bandholz AM, Bawle EV, Carmany EP, Powell CM, Hudson B, Schultz RA, Shaffer LG, Ballif BC. Investigation of TBR1 Hemizygosity: Four Individuals with 2q24 Microdeletions. Mol Syndromol 2012; 3:102-112. [PMID: 23112752 DOI: 10.1159/000342008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2012] [Indexed: 12/19/2022] Open
Abstract
TBR1 encodes a transcription factor with critical roles in corticogenesis, including cortical neuron migration and axon pathfinding, establishment of regional and laminar identity of cortical neurons, and control of glutamatergic neuronal cell fate. Based upon TBR1's role in cortical development, we sought to investigate TBR1 hemizygosity in individuals referred for genetic evaluation of intellectual disability and developmental delay. We describe 4 patients with microdeletions identified by molecular cytogenetic techniques, encompassing TBR1 and spanning 2q24.1q31.1, ranging in size from 2.17 to 12.34 Mb. Only the patient with the largest deletion had a possible cortical malformation. Mild ventriculomegaly is the only common brain anomaly, present in all patients; a Chiari I malformation is seen in 2 patients, and mega cisterna magna is seen in a third. Our findings are consistent with Tbr1 mouse models showing that hemizygosity of the gene requires additional genetic factors for the manifestation of severe structural brain malformations. Other syndromic features are present in these patients, including autism spectrum disorders, ocular colobomas, and craniosynostosis, features that are likely affected by the deletion of genes other than TBR1.
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Affiliation(s)
- R N Traylor
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, Wash., USA
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50
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Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn 2012; 32:976-85. [PMID: 22865506 PMCID: PMC3491694 DOI: 10.1002/pd.3945] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/11/2012] [Accepted: 07/01/2012] [Indexed: 01/12/2023]
Abstract
Objective To demonstrate the usefulness of microarray testing in prenatal diagnosis based on our laboratory experience. Methods Prenatal samples received from 2004 to 2011 for a variety of indications (n = 5003) were tested using comparative genomic hybridization-based microarrays targeted to known chromosomal syndromes with later versions of the microarrays providing backbone coverage of the entire genome. Results The overall detection rate of clinically significant copy number alterations (CNAs) among unbiased, nondemise cases was 5.3%. Detection rates were 6.5% and 8.2% for cases referred with abnormal ultrasounds and fetal demise, respectively. The overall rate of findings with unclear clinical significance was 4.2% but would reduce to 0.39% if only de novo CNAs were considered. In cases with known chromosomal rearrangements in the fetus or parent, 41.1% showed CNAs related to the rearrangements, whereas 1.3% showed clinically significant CNAs unrelated to the karyotype. Finally, 71% of the clinically significant CNAs found by microarray were below the resolution of conventional karyotyping of fetal chromosomes. Conclusions Microarray analysis has advantages over conventional cytogenetics, including the ability to more precisely characterize CNAs associated with abnormal karyotypes. Moreover, a significant proportion of cases studied by array will show a clinically significant CNA even with apparently normal karyotypes. © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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