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Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
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Kaul KL, Sabatini LM, Tsongalis GJ, Caliendo AM, Olsen RJ, Ashwood ER, Bale S, Benirschke R, Carlow D, Funke BH, Grody WW, Hayden RT, Hegde M, Lyon E, Murata K, Pessin M, Press RD, Thomson RB. The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care. Acad Pathol 2017; 4:2374289517708309. [PMID: 28815200 PMCID: PMC5528950 DOI: 10.1177/2374289517708309] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 12/16/2022] Open
Abstract
An explosion of knowledge and technology is revolutionizing medicine and patient care. Novel testing must be brought to the clinic with safety and accuracy, but also in a timely and cost-effective manner, so that patients can benefit and laboratories can offer testing consistent with current guidelines. Under the oversight provided by the Clinical Laboratory Improvement Amendments, laboratories have been able to develop and optimize laboratory procedures for use in-house. Quality improvement programs, interlaboratory comparisons, and the ability of laboratories to adjust assays as needed to improve results, utilize new sample types, or incorporate new mutations, information, or technologies are positive aspects of Clinical Laboratory Improvement Amendments oversight of laboratory-developed procedures. Laboratories have a long history of successful service to patients operating under Clinical Laboratory Improvement Amendments. A series of detailed clinical examples illustrating the quality and positive impact of laboratory-developed procedures on patient care is provided. These examples also demonstrate how Clinical Laboratory Improvement Amendments oversight ensures accurate, reliable, and reproducible testing in clinical laboratories.
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Affiliation(s)
- Karen L. Kaul
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Linda M. Sabatini
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Gregory J. Tsongalis
- Laboratory for Clinical Genomics and Advanced Technology, Department of Pathology, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
- Laboratory Medicine, Dartmouth Hitchcock Medical Center and Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Angela M. Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | | | | | - Robert Benirschke
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Dean Carlow
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Birgit H. Funke
- Laboratory for Molecular Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wayne W. Grody
- Departments of Pathology and Laboratory Medicine, Pediatrics and Human Genetics, UCLA School of Medicine, Los Angeles, CA, USA
| | - Randall T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Elaine Lyon
- Pathology Department, University of Utah School of Medicine/ARUP Laboratories, Salt Lake City, UT, USA
| | - Kazunori Murata
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard D. Press
- Department of Pathology and Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Richard B. Thomson
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Evanston, IL, USA
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Abstract
BACKGROUND We have recruited a group of four living and reviewed the records of six deceased distantly related French-Canadians of Acadian descent affected by a childhood-onset form of recessive limb-girdle muscular dystrophy (LGMD). All cases originate from the small archipelago of the Magdalen Islands (population: 13,000) isolated in the Gulf of St-Lawrence. METHODS Based on the likely sharing of the same founder mutation we completed a 319K SNPs genome-wide scan to identify the disease locus and then screen candidate genes in this region. RESULTS All patients had normal initial motor milestones. They presented with limb girdle weakness at the average age of seven years (5-11). Progressive weakness led to loss of ambulation at a wide range of ages (10-39). Patients also developed macroglossia, large calves and mild to moderate contractures, hyperlordosis and decreased pulmonary function. Creatine kinase levels were elevated (1,800-10,000 U/L) in the first decades, but decreased with progression of disease. Homozygosity mapping uncovered a shared chromosomal region of 6.33Mb. The alpha sarcoglycan (SGCA) gene, mutated in LGMD2D, lay in this candidate interval. Sequencing of all SGCA exons uncovered a shared homozygous missense mutation (c. 229C>T, p.R77C), the most common SGCA mutation internationally reported. Using demographic data, we estimated a high carrier rate of 1/22. CONCLUSION The p.R77C mutation has also been observed in many populations, including in France and Spain (Basques). This corresponds to the first reported recessive founder disease for the Magdalen Islands, an archipelago settled in the XIXth century, largely by Acadian immigrants.
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Black C, Said J. Normal vaginal delivery in a patient with autosomal recessive limb-girdle muscular dystrophy. Obstet Med 2010; 3:81-2. [PMID: 27582849 DOI: 10.1258/om.2010.090052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2010] [Indexed: 11/18/2022] Open
Abstract
The limb-girdle muscular dystrophies (LGMDs) are a group of genetically determined disorders of skeletal muscle, predominantly affecting the pelvic and shoulder-girdle musculature. The clinical course is variable but steadily progressive. Type 2A LGMD is the most frequent form, accounting for approximately 30% of identified cases. There are few reports of patients with Type 2A LGMD undergoing pregnancy and delivery. This case outlines a successful vaginal delivery in a woman with this condition.
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Affiliation(s)
- Carin Black
- The Royal Women's Hospital , Parkville, Victoria , Australia
| | - Joanne Said
- The Royal Women's Hospital , Parkville, Victoria , Australia
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Proximal muscle weakness in a 15-year-old boy. Semin Pediatr Neurol 2008; 15:186-9; discussion 189. [PMID: 19073325 DOI: 10.1016/j.spen.2008.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proximal muscle weakness, often indicative of a myopathy, has a broad differential diagnosis in children. We present a case of an adolescent boy with proximal weakness and a mildly elevated creatine kinase. He was found to have spinal muscular atrophy type III rather than a myopathy.
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