Title |
A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases
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Published in |
Genome Medicine, September 2015
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DOI | 10.1186/s13073-015-0221-8 |
Pubmed ID | |
Authors |
Neil A. Miller, Emily G. Farrow, Margaret Gibson, Laurel K. Willig, Greyson Twist, Byunggil Yoo, Tyler Marrs, Shane Corder, Lisa Krivohlavek, Adam Walter, Josh E. Petrikin, Carol J. Saunders, Isabelle Thiffault, Sarah E. Soden, Laurie D. Smith, Darrell L. Dinwiddie, Suzanne Herd, Julie A. Cakici, Severine Catreux, Mike Ruehle, Stephen F. Kingsmore |
Abstract |
While the cost of whole genome sequencing (WGS) is approaching the realm of routine medical tests, it remains too tardy to help guide the management of many acute medical conditions. Rapid WGS is imperative in light of growing evidence of its utility in acute care, such as in diagnosis of genetic diseases in very ill infants, and genotype-guided choice of chemotherapy at cancer relapse. In such situations, delayed, empiric, or phenotype-based clinical decisions may meet with substantial morbidity or mortality. We previously described a rapid WGS method, STATseq, with a sensitivity of >96 % for nucleotide variants that allowed a provisional diagnosis of a genetic disease in 50 h. Here improvements in sequencing run time, read alignment, and variant calling are described that enable 26-h time to provisional molecular diagnosis with >99.5 % sensitivity and specificity of genotypes. STATseq appears to be an appropriate strategy for acutely ill patients with potentially actionable genetic diseases. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 47 | 28% |
United Kingdom | 16 | 10% |
Spain | 11 | 7% |
Australia | 4 | 2% |
India | 4 | 2% |
Ireland | 3 | 2% |
Canada | 3 | 2% |
France | 3 | 2% |
Japan | 2 | 1% |
Other | 14 | 8% |
Unknown | 58 | 35% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 106 | 64% |
Scientists | 41 | 25% |
Practitioners (doctors, other healthcare professionals) | 13 | 8% |
Science communicators (journalists, bloggers, editors) | 5 | 3% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 5 | 2% |
United Kingdom | 4 | 2% |
Netherlands | 1 | <1% |
Italy | 1 | <1% |
Japan | 1 | <1% |
Luxembourg | 1 | <1% |
Unknown | 227 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 54 | 23% |
Student > Ph. D. Student | 51 | 21% |
Student > Master | 25 | 10% |
Other | 24 | 10% |
Student > Bachelor | 17 | 7% |
Other | 30 | 13% |
Unknown | 39 | 16% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 65 | 27% |
Agricultural and Biological Sciences | 51 | 21% |
Medicine and Dentistry | 27 | 11% |
Computer Science | 19 | 8% |
Engineering | 9 | 4% |
Other | 21 | 9% |
Unknown | 48 | 20% |