Whole exome sequencing is an efficient and sensitive method for detection of germline mutations in patients with phaeochromcytomas and paragangliomas
Open Access
- 19 September 2013
- journal article
- research article
- Published by Wiley in Clinical Endocrinology
- Vol. 80 (1), 25-33
- https://doi.org/10.1111/cen.12331
Abstract
Background Genetic testing is recommended when the probability of a disease‐associated germline mutation exceeds 10%. Germline mutations are found in approximately 25% of individuals with phaeochromcytoma (PCC) or paraganglioma (PGL); however, genetic heterogeneity for PCC/PGL means many genes may require sequencing. A phenotype‐directed iterative approach may limit costs but may also delay diagnosis, and will not detect mutations in genes not previously associated with PCC/PGL. Objective To assess whether whole exome sequencing (WES) was efficient and sensitive for mutation detection in PCC/PGL. Methods Whole exome sequencing was performed on blinded samples from eleven individuals with PCC/PGL and known mutations. Illumina TruSeq™ (Illumina Inc, San Diego, CA, USA) was used for exome capture of seven samples, and NimbleGen SeqCap EZ v3.0 (Roche NimbleGen Inc, Basel, Switzerland) for five samples (one sample was repeated). Massive parallel sequencing was performed on multiplexed samples. Sequencing data were called using Genome Analysis Toolkit and annotated using annovar. Data were assessed for coding variants in RET, NF1, VHL, SDHD, SDHB, SDHC, SDHA, SDHAF2, KIF1B, TMEM127, EGLN1 and MAX. Target capture of five exome capture platforms was compared. Results Six of seven mutations were detected using Illumina TruSeq™ exome capture. All five mutations were detected using NimbleGen SeqCap EZ v3.0 platform, including the mutation missed using Illumina TruSeq™ capture. Target capture for exons in known PCC/PGL genes differs substantially between platforms. Exome sequencing was inexpensive (<$A800 per sample for reagents) and rapid (results <5 weeks from sample reception). Conclusion Whole exome sequencing is sensitive, rapid and efficient for detection of PCC/PGL germline mutations. However, capture platform selection is critical to maximize sensitivity.Keywords
This publication has 37 references indexed in Scilit:
- Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing TechnologiesPLOS ONE, 2013
- Attenuated BMP1 Function Compromises Osteogenesis, Leading to Bone Fragility in Humans and ZebrafishAmerican Journal of Human Genetics, 2012
- Multicentric Carpotarsal Osteolysis Is Caused by Mutations Clustering in the Amino-Terminal Transcriptional Activation Domain of MAFBAmerican Journal of Human Genetics, 2012
- Analyzing and minimizing PCR amplification bias in Illumina sequencing librariesGenome Biology, 2011
- Genetic Testing for PheochromocytomaCurrent Hypertension Reports, 2010
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing dataGenome Research, 2010
- SDHA is a tumor suppressor gene causing paragangliomaHuman Molecular Genetics, 2010
- Germline mutations in TMEM127 confer susceptibility to pheochromocytomaNature Genetics, 2010
- SDH5 , a Gene Required for Flavination of Succinate Dehydrogenase, Is Mutated in ParagangliomaScience, 2009
- The kinesin KIF1Bβ acts downstream from EglN3 to induce apoptosis and is a potential 1p36 tumor suppressorGenes & Development, 2008