Identification of genetic variants using bar-coded multiplexed sequencing.

We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals at several Encyclopedia of DNA Elements (ENCODE) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms. For polymorphisms that were either previously identified within the Single Nucleotide Polymorphism database (dbSNP) or visually evident upon re-inspection of archived ENCODE traces, we observed a false positive rate of 11.3% using strict thresholds for predicting variants and 69.6% for lax thresholds. Conversely, false negative rates were 10.8-90.8%, with false negatives at stricter cut-offs occurring at lower coverage (<10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.

Arkansas Special Populations Access Network perception versus reality--cancer screening in primary care clinics.

The origin of cancer health disparities and mortality in Arkansas is multifactorial. In response to a cooperative agreement with the National Cancer Institute's Center to Reduce Cancer Health Disparities, the Arkansas Special Populations Access Network (ASPAN) was developed to reduce these disparities. ASPAN's partnership with local primary care physicians of the Arkansas Medical, Dental, and Pharmaceutical Association through the Cancer Education Awareness Program is the focus of this article. A quasi-experimental intervention, the Community Cancer Education Awareness Program, was employed that included 1) physician education to increase awareness of risk factors and cancer screening; and 2) patient education to increase screening, and 3) patient-generated screening questionnaires to prompt discussion of cancer risk and screening recommendations between patients and physicians. Two urban and 2 rural clinics were targeted during a 12-month period with interval intervention assessments. Baseline review of records (n = 200) from patients >/=40 were utilized to assess the rate of breast, prostate, and colorectal screenings among clinics. For the patient education intervention, patients (n = 120) were interviewed via a 34-item assessment. Physician awareness of cancer risk factors and screening recommendations significantly increased. Statistically significant increases were seen for prostate (P = .028), breast (P = .036), and colorectal (P < .001) cancer screening across all 4 clinics. Patients' increased likelihood of cancer screenings was associated with knowledge about consumption of animal fat (P < .001), dietary fiber (P < .013), and mammograms (P < .001). Utilizing the physician as the central change agent, the ASPAN provider network successfully enhanced cancer screening awareness of minority physicians and their patients. Cancer 2006. (c) 2006 American Cancer Society.

Identification of a D8S1179 primer binding site mutation and the validation of a primer designed to recover null alleles.

A population study of Chamorros and Filipinos using short tandem repeat (STR) loci amplified with the AmpFlSTR Profiler Plus PCR amplification kit demonstrated an excess of observed homozygosity at the D8S1179 locus. Use of a different set of D8S1179 primers to type the same samples did not demonstrate an excess of homozygosity and showed discordant genotypes at the D8S1179 locus. A single point mutation, G-to-A transition, 16 nucleotides from the 3' end of the reverse primer, was identified to cause allele dropout when using the AmpFlSTR Profiler Plus primer set. An additional D8S1179 reverse primer specific for the variant was constructed resulting in the recovery of the null allele. The primer was included in the newly developed AmpFlSTR Identifiler PCR amplification kit. No deleterious effects or non-specific peaks were observed in validation experiments evaluating primer concentration, Mg2+ concentration, annealing temperature and population samples.