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.
A distinctive renal lesion consisting of glomerulonephritis, diffuse tubular necrosis with regeneration, and interstitial inflammation was found in 49 biopsy/necropsy cases obtained from 1987 to 1992. This lesion is manifested clinically as a rapidly progressive glomerular disease that was uniformly fatal. Immune-mediated membranoproliferative glomerulonephritis predominated (43/49, 88%). Membranous glomerulonephritis (5/49, 10%) and amyloidosis (1/49, 2%) were also noted. Subendothelial deposits, IgG, IgM, and C3 were present along glomerular basement membranes. IgA was absent. The exact cause of the tubular necrosis is unknown. Affected dogs were significantly younger (5.6 +/- 2.6 years) than dogs with other forms of glomerulonephritis (7.1 +/- 3.6 years) and amyloidosis (7.8 +/- 3.5 years) both in the studied population for the same period and in the reported canine population. Labrador and Golden retrievers were 6.4 and 4.9 times more likely, respectively, to develop this lesion. This is the first report of a breed predilection for spontaneous canine glomerulonephritis. Previous reports have associated this lesion with Borrelia burgdorferi exposure. All dogs in this study were from Lyme disease-endemic areas. Of 18 dogs serologically tested, all were positive for exposure. Silver stain examination of kidneys revealed rare spirochetes, suggesting that the presence of spirochetes in the kidney is apparently unrelated to lesion development. The role of vaccination in development of the renal lesion is undetermined. The association of this histologically and clinically unique lesion, Lyme nephritis, with Borrelia burgdorferi infection is significant because it is the only fatal form of canine Lyme borreliosis.
DNA methylation, the only known covalent modification of mammalian DNA, occurs primarily in CpG dinucleotides. 51% of CpGs in the human genome reside within repeats, and 25% within Alu elements. Despite that, no method has been reported for large-scale ascertainment of CpG methylation in repeats. Here we describe a sequencing-based strategy for parallel determination of the CpG-methylation status of thousands of Alu repeats, and a computation algorithm to design primers that enable their specific amplification from bisulfite converted genomic DNA. Using a single primer pair, we generated amplicons of high sequence complexity, and derived CpG-methylation data from 31 178 Alu elements and their 5′ flanking sequences, altogether representing over 4 Mb of a human cerebellum epigenome. The analysis of the Alu methylome revealed that the methylation level of Alu elements is high in the intronic and intergenic regions, but low in the regions close to transcription start sites. Several hypomethylated Alu elements were identified and their hypomethylated status verified by pyrosequencing. Interestingly, some Alu elements exhibited a strikingly tissue-specific pattern of methylation. We anticipate the amplicons herein described to prove invaluable as epigenome representations, to monitor epigenomic alterations during normal development, in aging and in diseases such as cancer.
Exposure of phosphatidylserine (PtdSer) has been implicated in the recognition and phagocytosis of senescent and apoptotic cells, and CD36 has been proposed as one receptor protein that recognizes PtdSer and other anionic phospholipids. We investigated the binding of phospholipid vesicles to the monocytic leukemia cell lines THP-1 and J774A.1 with a flow cytometric assay; vesicles contained 50 mol% PtdSer, phosphatidylinositol (PtdIns), or phosphatidylglycerol (PtdGro), with the balance being phosphatidylcholine. Specific, high affinity binding was observed for vesicles containing PtdSer, PtdIns, or PtdGro. Specificity of the assay was confirmed by control experiments with erythrocytes, which showed minimal vesicle binding, and with annexin V, which blocked the binding of PtdSer, PtdGro, and PtdIns vesicles to the THP-1 cells. However, O-phospho-L-serine (to 1 mM) had no effect on the binding of PtdSer vesicles, indicating that high affinity binding requires a surface containing multiple phosphoserine groups rather than a single molecule. A monoclonal antibody to CD36 blocked up to 60% of the specific binding of PtdSer vesicles but had minimal to no effect on the binding of PtdGro or PtdIns vesicles. This antibody also selectively inhibited the phagocytosis of PtdSer-containing vesicles as measured by fluorescence microscopy, indicating that CD36 is functionally significant for phagocytosis of this vesicle type. In addition, collagen and thrombospondin, two other putative ligands of CD36, were unable to inhibit the binding of PtdSer vesicles. We conclude that CD36 is the primary protein responsible for the high affinity binding of PtdSer vesicles to these monocyte-like cells. In addition, CD36 appears to be specific for PtdSer among anionic phospholipids, and nonphospholipid ligands of CD36 do not share binding sites with PtdSer on CD36.Phospholipids are distributed asymmetrically between the two faces of the plasma membrane (1-3). In particular, PtdSer 1 is nearly absent from the extracellular face of the plasma membrane in resting cells. Membrane phospholipid asymmetry is maintained by the aminophospholipid translocase, an ATPdependent enzyme that transports PtdSer and phosphatidylethanolamine from the outer face to the inner face of the plasma membrane. This protein was recently cloned and shown to be a member of a new family of ATP-dependent transporters (4). Under some circumstances disruption of membrane asymmetry results in PtdSer exposure at the outer face of the membrane. This is an essential part of the normal platelet procoagulant response, and increased PtdSer exposure may also be a signal for clearance of damaged or senescent cells. More recently, increased exposure of PtdSer has emerged as a key early event in cells undergoing apoptosis (5-9). Given the earlier work suggesting a role for PtdSer exposure in triggering phagocytic removal of cells, exposure of PtdSer may mark apoptotic cells for phagocytic removal, either by specialized phagocytic cells or by their healthy neighbors.There are several ...
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