Molecular findings among patients referred for clinical whole-exome sequencing
Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to dise...
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| Vydané v: | JAMA : the journal of the American Medical Association Ročník 312; číslo 18; s. 1870 |
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| Hlavní autori: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
United States
12.11.2014
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| ISSN: | 1538-3598, 1538-3598 |
| On-line prístup: | Zistit podrobnosti o prístupe |
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| Abstract | Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.
To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.
Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.
Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.
A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.
Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients. |
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| AbstractList | Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.IMPORTANCEClinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.OBJECTIVETo perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome.Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.DESIGN, SETTING, AND PATIENTSObservational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay.Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.MAIN OUTCOMES AND MEASURESWhole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings.A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.RESULTSA molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics.Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients.CONCLUSIONS AND RELEVANCEWhole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients. Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders. To perform clinical whole-exome sequencing and report (1) the rate of molecular diagnosis among phenotypic groups, (2) the spectrum of genetic alterations contributing to disease, and (3) the prevalence of medically actionable incidental findings such as FBN1 mutations causing Marfan syndrome. Observational study of 2000 consecutive patients with clinical whole-exome sequencing analyzed between June 2012 and August 2014. Whole-exome sequencing tests were performed at a clinical genetics laboratory in the United States. Results were reported by clinical molecular geneticists certified by the American Board of Medical Genetics and Genomics. Tests were ordered by the patient's physician. The patients were primarily pediatric (1756 [88%]; mean age, 6 years; 888 females [44%], 1101 males [55%], and 11 fetuses [1% gender unknown]), demonstrating diverse clinical manifestations most often including nervous system dysfunction such as developmental delay. Whole-exome sequencing diagnosis rate overall and by phenotypic category, mode of inheritance, spectrum of genetic events, and reporting of incidental findings. A molecular diagnosis was reported for 504 patients (25.2%) with 58% of the diagnostic mutations not previously reported. Molecular diagnosis rates for each phenotypic category were 143/526 (27.2%; 95% CI, 23.5%-31.2%) for the neurological group, 282/1147 (24.6%; 95% CI, 22.1%-27.2%) for the neurological plus other organ systems group, 30/83 (36.1%; 95% CI, 26.1%-47.5%) for the specific neurological group, and 49/244 (20.1%; 95% CI, 15.6%-25.8%) for the nonneurological group. The Mendelian disease patterns of the 527 molecular diagnoses included 280 (53.1%) autosomal dominant, 181 (34.3%) autosomal recessive (including 5 with uniparental disomy), 65 (12.3%) X-linked, and 1 (0.2%) mitochondrial. Of 504 patients with a molecular diagnosis, 23 (4.6%) had blended phenotypes resulting from 2 single gene defects. About 30% of the positive cases harbored mutations in disease genes reported since 2011. There were 95 medically actionable incidental findings in genes unrelated to the phenotype but with immediate implications for management in 92 patients (4.6%), including 59 patients (3%) with mutations in genes recommended for reporting by the American College of Medical Genetics and Genomics. Whole-exome sequencing provided a potential molecular diagnosis for 25% of a large cohort of patients referred for evaluation of suspected genetic conditions, including detection of rare genetic events and new mutations contributing to disease. The yield of whole-exome sequencing may offer advantages over traditional molecular diagnostic approaches in certain patients. |
| Author | Ding, Yan Plon, Sharon E Muzny, Donna M Chiang, Theodore Walkiewicz, Magdalena Bekheirnia, Mir Reza Beuten, Joke Yang, Yaping Veeraraghavan, Narayanan Buhay, Christian Leduc, Magalie He, Weimin Stray-Pedersen, Asbjorg Cui, Hong Zhang, Jing Boerwinkle, Eric Gibbs, Richard A Craigen, William J Braxton, Alicia Patel, Ankita Xia, Fan Lupski, James R Scull, Jennifer Liu, Pengfei Beaudet, Arthur L Wen, Shu Reid, Jeffrey Hawes, Alicia Person, Richard Niu, Zhiyv Bainbridge, Matthew Eng, Christine M Alcaraz, Wendy Landsverk, Megan Ward, Patricia Wang, Min Willis, Alecia |
| Author_xml | – sequence: 1 givenname: Yaping surname: Yang fullname: Yang, Yaping organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 2 givenname: Donna M surname: Muzny fullname: Muzny, Donna M organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 3 givenname: Fan surname: Xia fullname: Xia, Fan organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 4 givenname: Zhiyv surname: Niu fullname: Niu, Zhiyv organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 5 givenname: Richard surname: Person fullname: Person, Richard organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 6 givenname: Yan surname: Ding fullname: Ding, Yan organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 7 givenname: Patricia surname: Ward fullname: Ward, Patricia organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 8 givenname: Alicia surname: Braxton fullname: Braxton, Alicia organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 9 givenname: Min surname: Wang fullname: Wang, Min organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 10 givenname: Christian surname: Buhay fullname: Buhay, Christian organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 11 givenname: Narayanan surname: Veeraraghavan fullname: Veeraraghavan, Narayanan organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 12 givenname: Alicia surname: Hawes fullname: Hawes, Alicia organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 13 givenname: Theodore surname: Chiang fullname: Chiang, Theodore organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 14 givenname: Magalie surname: Leduc fullname: Leduc, Magalie organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 15 givenname: Joke surname: Beuten fullname: Beuten, Joke organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 16 givenname: Jing surname: Zhang fullname: Zhang, Jing organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 17 givenname: Weimin surname: He fullname: He, Weimin organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 18 givenname: Jennifer surname: Scull fullname: Scull, Jennifer organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 19 givenname: Alecia surname: Willis fullname: Willis, Alecia organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 20 givenname: Megan surname: Landsverk fullname: Landsverk, Megan organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 21 givenname: William J surname: Craigen fullname: Craigen, William J organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas – sequence: 22 givenname: Mir Reza surname: Bekheirnia fullname: Bekheirnia, Mir Reza organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 23 givenname: Asbjorg surname: Stray-Pedersen fullname: Stray-Pedersen, Asbjorg organization: Department of Pediatrics, Baylor College of Medicine, Houston, Texas – sequence: 24 givenname: Pengfei surname: Liu fullname: Liu, Pengfei organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 25 givenname: Shu surname: Wen fullname: Wen, Shu organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 26 givenname: Wendy surname: Alcaraz fullname: Alcaraz, Wendy organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 27 givenname: Hong surname: Cui fullname: Cui, Hong organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 28 givenname: Magdalena surname: Walkiewicz fullname: Walkiewicz, Magdalena organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 29 givenname: Jeffrey surname: Reid fullname: Reid, Jeffrey organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 30 givenname: Matthew surname: Bainbridge fullname: Bainbridge, Matthew organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 31 givenname: Ankita surname: Patel fullname: Patel, Ankita organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 32 givenname: Eric surname: Boerwinkle fullname: Boerwinkle, Eric organization: Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas4Human Genetics Center, University of Texas Health Science Center, Houston – sequence: 33 givenname: Arthur L surname: Beaudet fullname: Beaudet, Arthur L organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas – sequence: 34 givenname: James R surname: Lupski fullname: Lupski, James R organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas – sequence: 35 givenname: Sharon E surname: Plon fullname: Plon, Sharon E organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas3Department of Pediatrics, Baylor College of Medicine, Houston, Texas – sequence: 36 givenname: Richard A surname: Gibbs fullname: Gibbs, Richard A organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas2Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas – sequence: 37 givenname: Christine M surname: Eng fullname: Eng, Christine M organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25326635$$D View this record in MEDLINE/PubMed |
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| Snippet | Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.
To perform clinical whole-exome... Clinical whole-exome sequencing is increasingly used for diagnostic evaluation of patients with suspected genetic disorders.IMPORTANCEClinical whole-exome... |
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| SubjectTerms | Adolescent Adult Child Child, Preschool Exome Female Fetus Genetic Diseases, Inborn - diagnosis Genetic Testing Genomics Humans Incidental Findings Infant Infant, Newborn Male Molecular Diagnostic Techniques Mutation Phenotype Referral and Consultation Sequence Analysis, DNA - methods |
| Title | Molecular findings among patients referred for clinical whole-exome sequencing |
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