Title |
Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing
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Published in |
BMC Medical Genomics, May 2014
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DOI | 10.1186/1755-8794-7-23 |
Pubmed ID | |
Authors |
Stephen Q Wong, Jason Li, Angela Y-C Tan, Ravikiran Vedururu, Jia-Min B Pang, Hongdo Do, Jason Ellul, Ken Doig, Anthony Bell, Grant A McArthur, Stephen B Fox, David M Thomas, Andrew Fellowes, John P Parisot, Alexander Dobrovic |
Abstract |
Clinical specimens undergoing diagnostic molecular pathology testing are fixed in formalin due to the necessity for detailed morphological assessment. However, formalin fixation can cause major issues with molecular testing, as it causes DNA damage such as fragmentation and non-reproducible sequencing artefacts after PCR amplification. In the context of massively parallel sequencing (MPS), distinguishing true low frequency variants from sequencing artefacts remains challenging. The prevalence of formalin-induced DNA damage and its impact on molecular testing and clinical genomics remains poorly understood. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 1 | 20% |
Canada | 1 | 20% |
Australia | 1 | 20% |
Germany | 1 | 20% |
Israel | 1 | 20% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 4 | 80% |
Members of the public | 1 | 20% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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Australia | 2 | <1% |
United States | 2 | <1% |
Canada | 2 | <1% |
Netherlands | 1 | <1% |
Czechia | 1 | <1% |
Ireland | 1 | <1% |
Germany | 1 | <1% |
United Kingdom | 1 | <1% |
Unknown | 248 | 96% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 56 | 22% |
Student > Master | 40 | 15% |
Student > Ph. D. Student | 33 | 13% |
Student > Bachelor | 22 | 8% |
Other | 20 | 8% |
Other | 34 | 13% |
Unknown | 54 | 21% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 80 | 31% |
Medicine and Dentistry | 56 | 22% |
Agricultural and Biological Sciences | 45 | 17% |
Engineering | 7 | 3% |
Computer Science | 6 | 2% |
Other | 15 | 6% |
Unknown | 50 | 19% |