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      Systematic Classification of Disease Severity for Evaluation of Expanded Carrier Screening Panels

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          Abstract

          Professional guidelines dictate that disease severity is a key criterion for carrier screening. Expanded carrier screening, which tests for hundreds to thousands of mutations simultaneously, requires an objective, systematic means of describing a given disease's severity to build screening panels. We hypothesized that diseases with characteristics deemed to be of highest impact would likewise be rated as most severe, and diseases with characteristics of lower impact would be rated as less severe. We describe a pilot test of this hypothesis in which we surveyed 192 health care professionals to determine the impact of specific disease phenotypic characteristics on perceived severity, and asked the same group to rate the severity of selected inherited diseases. The results support the hypothesis: we identified four “Tiers” of disease characteristics (1–4). Based on these responses, we developed an algorithm that, based on the combination of characteristics normally seen in an affected individual, classifies the disease as Profound, Severe, Moderate, or Mild. This algorithm allows simple classification of disease severity that is replicable and not labor intensive.

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          Most cited references2

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          High-Throughput Carrier Screening Using TaqMan Allelic Discrimination

          Members of the Ashkenazi Jewish community are at an increased risk for inheritance of numerous genetic diseases such that carrier screening is medically recommended. This paper describes the development and evaluation of 30 TaqMan allelic discrimination qPCR assays for 29 mutations on 2 different high-throughput platforms. Four of these mutations are in the GBA gene and are successfully examined using short amplicons due to the qualitative nature of TaqMan allelic discrimination. Two systems were tested for their reliability (call rate) and consistency with previous diagnoses (diagnostic accuracy) indicating a call rate of 99.04% and a diagnostic accuracy of 100% (+/−0.00%) from one platform, and a call rate of 94.66% and a diagnostic accuracy of 93.35% (+/−0.29%) from a second for 9,216 genotypes. Results for mutations tested at the expected carrier frequency indicated a call rate of 97.87% and a diagnostic accuracy of 99.96% (+/−0.05%). This study demonstrated the ability of a high throughput qPCR methodology to accurately and reliably genotype 29 mutations in parallel. The universally applicable nature of this technology provides an opportunity to increase the number of mutations that can be screened simultaneously, and reduce the cost and turnaround time for accommodating newly identified and clinically relevant mutations.
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            Genotyping microarray for the detection of more than 200 CFTR mutations in ethnically diverse populations.

            Cystic fibrosis (CF), which is due to mutations in the cystic fibrosis transmembrane conductance regulator gene, is a common life-shortening disease. Although CF occurs with the highest incidence in Caucasians, it also occurs in other ethnicities with variable frequency. Recent national guidelines suggest that all couples contemplating pregnancy should be informed of molecular screening for CF carrier status for purposes of genetic counseling. Commercially available CF carrier screening panels offer a limited panel of mutations, however, making them insufficiently sensitive for certain groups within an ethnically diverse population. This discrepancy is even more pronounced when such carrier screening panels are used for diagnostic purposes. By means of arrayed primer extension technology, we have designed a genotyping microarray with 204 probe sites for CF transmembrane conductance regulator gene mutation detection. The arrayed primer extension array, based on a platform technology for disease detection with multiple applications, is a robust, cost-effective, and easily modifiable assay suitable for CF carrier screening and disease detection.
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              Author and article information

              Contributors
              Role: Editor
              Journal
              PLoS One
              PLoS ONE
              plos
              plosone
              PLoS ONE
              Public Library of Science (San Francisco, USA )
              1932-6203
              2014
              10 December 2014
              16 December 2014
              : 9
              : 12
              : e114391
              Affiliations
              [1]Counsyl, South San Francisco, California, United States of America
              Stavanger University Hospital, Norway
              Author notes

              Competing Interests: The authors study was self-funded by Counsyl, a molecular genetics laboratory that performs carrier screening. All but one author (FH) are currently employed by Counsyl. FH was employed by Counsyl at the time of study design, data collection and data analysis. No other outside funding was provided. This does not alter the authors' adherence to PLOS ONE policies and sharing data and materials.

              Conceived and designed the experiments: FH GAL EE IH. Performed the experiments: FH GAL EAP NC. Analyzed the data: FH GAL EE IH. Contributed reagents/materials/analysis tools: FH GAL EAP NC. Wrote the paper: FH GAL EE IH.

              Article
              PONE-D-13-50993
              10.1371/journal.pone.0114391
              4262393
              25494330
              3ea3e0b9-e2a7-4970-854f-32a1efc6b462
              Copyright @ 2014

              This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

              History
              : 9 December 2013
              : 9 November 2014
              Page count
              Pages: 15
              Funding
              This study was funded by Counsyl, a molecular genetics laboratory that performs carrier screening. Study design, data collection and analysis, and manuscript preparation were all completed by the authors who are currently, or were, employees at Counsyl.
              Categories
              Research Article
              Biology and Life Sciences
              Computational Biology
              Genome Analysis
              Developmental Biology
              Fibrosis
              Cystic Fibrosis
              Genetics
              Gene Identification and Analysis
              Genetic Screens
              Genetic Dominance
              Recessive Traits
              Autosomal Recessive Traits
              Genomics
              Genomic Medicine
              Genetic Counseling
              Genetic Testing
              Genetics of Disease
              Heredity
              Human Genetics
              Molecular Genetics
              Mutation
              Medicine and Health Sciences
              Clinical Genetics
              Diagnostic Medicine
              Health Care
              Health Care Policy
              Screening Guidelines
              Pathology and Laboratory Medicine
              Clinical Pathology
              Public and Occupational Health
              Health Screening
              Women's Health
              Obstetrics and Gynecology

              Uncategorized
              Uncategorized

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