The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

/pdf/gapped-blast-and-psi-blast-a-new-generation-of-protein-2ybl67x5yx.pdf

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

A strong candidate for the 17q-linked BRCA1 gene, which influences susceptibility to breast and ovarian cancer, has been identified by positional cloning methods. Probable predisposing mutations have been detected in five of eight kindreds presumed to segregate BRCA1 susceptibility alleles. The mutations include an 11-base pair deletion, a 1-base pair insertion, a stop codon, a missense substitution, and an inferred regulatory mutation. The BRCA1 gene is expressed in numerous tissues, including breast and ovary, and encodes a predicted protein of 1863 amino acids. This protein contains a zinc finger domain in its amino-terminal region, but is otherwise unrelated to previously described proteins. Identification of BRCA1 should facilitate early diagnosis of breast and ovarian cancer susceptibility in some individuals as well as a better understanding of breast cancer biology.

https://courses.washington.edu/gs466/readings/miki.pdf

A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

Germline mutations in BRCA1 and BRCA2 confer high risks of breast and ovarian cancer, but the average magnitude of these risks is uncertain and may depend on the context. Estimates based on multiple-case families may be enriched for mutations of higher risk and/or other familial risk factors, whereas risk estimates from studies based on cases unselected for family history have been imprecise. We pooled pedigree data from 22 studies involving 8,139 index case patients unselected for family history with female (86%) or male (2%) breast cancer or epithelial ovarian cancer (12%), 500 of whom had been found to carry a germline mutation in BRCA1 or BRCA2. Breast and ovarian cancer incidence rates for mutation carriers were estimated using a modified segregation analysis, based on the occurrence of these cancers in the relatives of mutation-carrying index case patients. The average cumulative risks in BRCA1-mutation carriers by age 70 years were 65% (95% confidence interval 44%-78%) for breast cancer and 39% (18%-54%) for ovarian cancer. The corresponding estimates for BRCA2 were 45% (31%-56%) and 11% (2.4%-19%). Relative risks of breast cancer declined significantly with age for BRCA1-mutation carriers (P trend.0012) but not for BRCA2-mutation carriers. Risks in carriers were higher when based on index breast cancer cases diagnosed at <35 years of age. We found some evidence for a reduction in risk in women from earlier birth cohorts and for variation in risk by mutation position for both genes. The pattern of cancer risks was similar to those found in multiple-case families, but their absolute magnitudes were lower, particularly for BRCA2. The variation in risk by age at diagnosis of index case is consistent with the effects of other genes modifying cancer risk in carriers.

https://www.cell.com/ajhg/pdf/S0002-9297(07)60640-5.pdf

Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies

A central aim of cancer research has been to identify the mutated genes that are causally implicated in oncogenesis ('cancer genes'). After two decades of searching, how many have been identified and how do they compare to the complete gene set that has been revealed by the human genome sequence? We have conducted a 'census' of cancer genes that indicates that mutations in more than 1% of genes contribute to human cancer. The census illustrates striking features in the types of sequence alteration, cancer classes in which oncogenic mutations have been identified and protein domains that are encoded by cancer genes.

A census of human cancer genes

Supplementary file 2.

17q-linked breast cancer susceptibility gene and ovarian

17Q-Linked ovarian and breast cancer susceptibility gene

Background. COSMIC (http://www.sanger.ac.uk/cosmic) is a system designed to curate the world's literature on somatic mutations in known cancer genes. Initially conceived to capture the mutation spread in point-mutated genes, COSMIC has now grown to encompass gene fusion products of genome rearrangement events which generate completely novel transcripts, together with all the somatic mutation data from candidate gene screens at the Cancer Genome Project, UK (CGP), covering almost 5000 genes of potential interest in cancer genetics. Results. The latest release of COSMIC (version 37; July 2008) now holds full and up-to-date curation of over 5,900 scientific papers, examining over 268,000 tumours, in which over 59,000 mutations are detailed through 60 pointmutated genes. Fusion gene products have been curated for 16 pairs of genes, described through over 4200 tumours. 2246 papers were rejected during manual curation, usually due to significant inconsistencies in the publication. A relational database holds the captured information, which is warehoused for each release. The information is presented on the internet with a series of graphical and tabulated views aiding navigation and interpretation. Conclusions. The current version of COSMIC is close to fulfilling its original intentions, with curation of most pointmutated genes in cancer complete. However, new challenges are emerging with the need to calculate the effect of high numbers of observed sequence changes to identify those driving tumour formation, and the need to meaningfully handle the increasing quantities of data from high-throughput screens and next-generation sequencing technologies.

/pdf/cosmic-curating-the-cancer-variome-47demaawpb.pdf

COSMIC, curating the cancer variome

La presente invention concerne generalement le domaine de la genetique humaine. De maniere plus specifique, la presente invention concerne des procedes et des materiaux utilises pour isoler et detecter un gene humain de predisposition au cancer du sein et des ovaires (BRCA1), dont certains alleles mutants provoquent la sensibilite au cancer, en particulier, au cancer du sein et des ovaires. De maniere particuliere, l'invention concerne les mutations de lignees germinales dans le gene BRCA1 et leur utilisation pour diagnostiquer la predisposition au cancer du sein et des ovaires. La presente invention concerne, en outre, des mutations somatiques du gene BRCA1 dans le cancer humain du sein et des ovaires, et leur utilisation pour diagnostiquer et prognostiquer un cancer humain du sein et des ovaires. En outre, l'invention concerne des mutations somatiques dans le gene BRCA1 dans d'autres cancers humains et leur utilisation pour diagnostiquer et prognostiquer les cancers humains. L'invention traite aussi de la therapie des cancers humains qui presentent une mutation du gene BRCA1, y compris de la therapie genique, de la therapie par remplacement de proteines et de mimetismes de proteines. L'invention concerne egalement le criblage des medicaments utilises dans la therapie du cancer. Enfin, l'invention a pour objet le criblage du gene BRCA1 afin d'y detecter des mutations, qui permettent de diagnostiquer la predisposition au cancer du sein et des ovaires.

P. Andrew Futreal

Papers

Supplementary file 2.

17q-linked breast cancer susceptibility gene and ovarian

17Q-Linked ovarian and breast cancer susceptibility gene

COSMIC, curating the cancer variome

Procede pour diagnostiquer une predisposition au cancer du sein et des ovaires