Recent years have seen development and implementation of anticancer therapies targeted to particular gene mutations, but methods to assay clinical cancer specimens in a comprehensive way for the critical mutations remain underdeveloped. We have developed UW-OncoPlex, a clinical molecular diagnostic assay to provide simultaneous deep-sequencing information, based on >500× average coverage, for all classes of mutations in 194 clinically relevant genes. To validate UW-OncoPlex, we tested 98 previously characterized clinical tumor specimens from 10 different cancer types, including 41 formalin-fixed paraffin-embedded tissue samples. Mixing studies indicated reliable mutation detection in samples with ≥ 10% tumor cells. In clinical samples with ≥ 10% tumor cells, UW-OncoPlex correctly identified 129 of 130 known mutations [sensitivity 99.2%, (95% CI, 95.8%-99.9%)], including single nucleotide variants, small insertions and deletions, internal tandem duplications, gene copy number gains and amplifications, gene copy losses, chromosomal gains and losses, and actionable genomic rearrangements, including ALK-EML4, ROS1, PML-RARA, and BCR-ABL. In the same samples, the assay also identified actionable point mutations in genes not previously analyzed and novel gene rearrangements of MLL and GRIK4 in melanoma, and of ASXL1, PIK3R1, and SGCZ in acute myeloid leukemia. To best guide existing and emerging treatment regimens and facilitate integration of genomic testing with patient care, we developed a framework for data analysis, decision support, and reporting clinically actionable results.

A hypermutated subtype of advanced prostate cancer was recently described, but prevalence and mechanisms have not been well-characterized. Here we find that 12% (7 of 60) of advanced prostate cancers are hypermutated, and that all hypermutated cancers have mismatch repair gene mutations and microsatellite instability (MSI). Mutations are frequently complex MSH2 or MSH6 structural rearrangements rather than MLH1 epigenetic silencing. Our findings identify parallels and differences in the mechanisms of hypermutation in prostate cancer compared with other MSI-associated cancers.

Lynch syndrome (hereditary nonpolyposis colon cancer) and adenomatous polyposis syndromes frequently have overlapping clinical features. Current approaches for molecular genetic testing are often stepwise, taking a best-candidate gene approach with testing of additional genes if initial results are negative. We report a comprehensive assay called ColoSeq that detects all classes of mutations in Lynch and polyposis syndrome genes using targeted capture and massively parallel next-generation sequencing on the Illumina HiSeq2000 instrument. In blinded specimens and colon cancer cell lines with defined mutations, ColoSeq correctly identified 28/28 (100%) pathogenic mutations in MLH1, MSH2, MSH6, PMS2, EPCAM, APC, and MUTYH, including single nucleotide variants (SNVs), small insertions and deletions, and large copy number variants. There was 100% reproducibility of detection mutation between independent runs. The assay correctly identified 222 of 224 heterozygous SNVs (99.4%) in HapMap samples, demonstrating high sensitivity of calling all variants across each captured gene. Average coverage was greater than 320 reads per base pair when the maximum of 96 index samples with barcodes were pooled. In a specificity study of 19 control patients without cancer from different ethnic backgrounds, we did not find any pathogenic mutations but detected two variants of uncertain significance. ColoSeq offers a powerful, cost-effective means of genetic testing for Lynch and polyposis syndromes that eliminates the need for stepwise testing and multiple follow-up clinical visits.

Discussion:The low enrollment rate suggests that the program was not feasible or acceptable. Alternative approaches are needed to improve the reach and efficacy of cessation interventions for Alaska Native women. IntroductionTobacco use during pregnancy is a major public health problem in the United States. Estimates of smoking prevalence during pregnancy among U.S. women range from 11% to 22% (Goodwin, Keyes, & Simuro, 2007;L. T. Martin, McNamara, et al., 2008). Among U.S. women who gave birth in 2005, the smoking rates during pregnancy were American Indian and Alaska Native (AI/ AN) women (18%), non-Hispanic White (14%), non-Hispanic Black (9%), Hispanic (3%), and Asian women (2%; Substance Abuse and Mental Services Administration [SAMHSA], 2007). Smoking during pregnancy is the leading preventable cause of low infant birth weight and is associated with other maternal and infant adverse perinatal events (Cnattingius, 2004). Less than 1% of U.S. women report smokeless tobacco (ST) use during pregnancy (SAMHSA, 2007). A number of studies report potential adverse health risks of ST use during pregnancy for both the mother and infant including increased risk for preterm birth, stillbirth, and low birth weight (England et al., 2003;Gupta & Subramoney, 2006;Steyn, de Wet, Saloojee, Nel, & Yach, 2006). AbstractBackground: Among Alaska Native women residing in the Yukon-Kuskokwim (Y-K) Delta region of Western Alaska, about 79% smoke cigarettes or use smokeless tobacco during pregnancy. Treatment methods developed and evaluated among Alaska Native pregnant tobacco users do not exist. This pilot study used a randomized two-group design to assess the feasibility and acceptability of a targeted cessation intervention for Alaska Native pregnant women. Methods:Recruitment occurred over an 8-month period. Enrolled participants were randomly assigned to the control group (n = 18; brief face-to-face counseling at the first visit and written materials) or to the intervention group (n = 17) consisting of faceto-face counseling at the first visit, four telephone calls, a video highlighting personal stories, and a cessation guide. Interviewbased assessments were conducted at baseline and follow-up during pregnancy (≥60 days postrandomization). Feasibility was determined by the recruitment and retention rates. Results:The participation rate was very low with only 12% of eligible women (35/293) enrolled. Among enrolled participants, the study retention rates were high in both the intervention (71%) and control (94%) groups. The biochemically confirmed abstinence rates at follow-up were 0% and 6% for the intervention and control groups, respectively.