High-density oligonucleotide-based resequencing assay for mutations causing syndromic and non-syndromic forms of thoracic aortic aneurysms and dissections
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High-density oligonucleotide-based resequencing assay for mutations causing syndromic and non-syndromic forms of thoracic aortic aneurysms and dissections. / Kathiravel, Ushanthine; Keyser, Britta; Hoffjan, Sabine; Kötting, Judith; Müller, Melanie; Sivalingam, Sugirthan; Bonin, Michael; Arslan-Kirchner, Mine; von Kodolitsch, Yskert; Binner, Priska; Scheffold, Thomas; Stuhrmann, Manfred; Waldmüller, Stephan.
In: MOL CELL PROBE, Vol. 27, No. 2, 04.2013, p. 103-108.Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review
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TY - JOUR
T1 - High-density oligonucleotide-based resequencing assay for mutations causing syndromic and non-syndromic forms of thoracic aortic aneurysms and dissections
AU - Kathiravel, Ushanthine
AU - Keyser, Britta
AU - Hoffjan, Sabine
AU - Kötting, Judith
AU - Müller, Melanie
AU - Sivalingam, Sugirthan
AU - Bonin, Michael
AU - Arslan-Kirchner, Mine
AU - von Kodolitsch, Yskert
AU - Binner, Priska
AU - Scheffold, Thomas
AU - Stuhrmann, Manfred
AU - Waldmüller, Stephan
N1 - Copyright © 2012 Elsevier Ltd. All rights reserved.
PY - 2013/4
Y1 - 2013/4
N2 - Thoracic aortic aneurysm and dissection is associated with increasing mortality rate that may occur as part of a syndrome or as an isolated familial condition. Several genes have been implicated in causing TAAD, though an appropriate genetic test for their parallel testing is not yet available. Herein, we describe the novel 117-kb "MFSTAAD chip" that may help to understand the genetic basis of TAAD. A custom duplicate resequencing assay was developed to cover eight genes previously described in TAAD; FBN1, TGFBR1&2, COL3A1, MYH11, ACTA2, SLC2A10 and NOTCH1. GSEQ and SeqC software were used for data analysis. The analytical sensitivity of the assay was validated by the recognition of 182 known mutations (153 point mutations, 21 deletions, 7 insertions and 1 duplication) and a cohort of 28 patients were selected to determine the mutation yield, whereby 18 of them were previously negative for mutations in the genes FBN1 and TGFBR2. The assay had significantly higher sensitivity for point mutations (100%) and the largest deletion of 16 bp was detectable through a decline in the hybridization strength. The overall analytical sensitivity was 85%. Mutation testing of 28 unrelated TAAD patients revealed 4 known and 6 possibly pathogenic mutations with a mutation yield of 32%. The MFSTAAD chip is an alternative tool to next-generation sequencing that allows parallel analysis of several genes on a single platform. Refinements in the probe design and data analysis software will increase the analytical sensitivity of insertions and deletions making this assay even more applicable for clinical testing.
AB - Thoracic aortic aneurysm and dissection is associated with increasing mortality rate that may occur as part of a syndrome or as an isolated familial condition. Several genes have been implicated in causing TAAD, though an appropriate genetic test for their parallel testing is not yet available. Herein, we describe the novel 117-kb "MFSTAAD chip" that may help to understand the genetic basis of TAAD. A custom duplicate resequencing assay was developed to cover eight genes previously described in TAAD; FBN1, TGFBR1&2, COL3A1, MYH11, ACTA2, SLC2A10 and NOTCH1. GSEQ and SeqC software were used for data analysis. The analytical sensitivity of the assay was validated by the recognition of 182 known mutations (153 point mutations, 21 deletions, 7 insertions and 1 duplication) and a cohort of 28 patients were selected to determine the mutation yield, whereby 18 of them were previously negative for mutations in the genes FBN1 and TGFBR2. The assay had significantly higher sensitivity for point mutations (100%) and the largest deletion of 16 bp was detectable through a decline in the hybridization strength. The overall analytical sensitivity was 85%. Mutation testing of 28 unrelated TAAD patients revealed 4 known and 6 possibly pathogenic mutations with a mutation yield of 32%. The MFSTAAD chip is an alternative tool to next-generation sequencing that allows parallel analysis of several genes on a single platform. Refinements in the probe design and data analysis software will increase the analytical sensitivity of insertions and deletions making this assay even more applicable for clinical testing.
KW - Aneurysm, Dissecting/genetics
KW - Aortic Aneurysm, Thoracic/genetics
KW - Base Sequence
KW - Computer Simulation
KW - DNA Mutational Analysis/instrumentation
KW - False Positive Reactions
KW - Fibrillin-1
KW - Fibrillins
KW - Genetic Predisposition to Disease
KW - Humans
KW - Microfilament Proteins/genetics
KW - Molecular Sequence Data
KW - Mutation
KW - Oligonucleotide Array Sequence Analysis/methods
KW - Oligonucleotides
KW - Sensitivity and Specificity
U2 - 10.1016/j.mcp.2012.10.002
DO - 10.1016/j.mcp.2012.10.002
M3 - SCORING: Journal article
C2 - 23142374
VL - 27
SP - 103
EP - 108
JO - MOL CELL PROBE
JF - MOL CELL PROBE
SN - 0890-8508
IS - 2
ER -