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Purpose: To investigate pan-ethnic SMN1 copy-number and sequence variation by hybridization-based target enrichment coupled with massively parallel sequencing or next-generation sequencing (NGS). Methods: NGS reads aligned to SMN1 and SMN2 exon 7 were quantified to determine the total combined copy number of SMN1 and SMN2 . The ratio of SMN1 to SMN2 was calculated based on a single-nucleotide difference that distinguishes the two genes. SMN1 copy-number results were compared between the NGS and quantitative polymerase chain reaction and/or multiplex ligation-dependent probe amplification. The NGS data set was also queried for the g.27134T>G single-nucleotide polymorphism (SNP) and other SMN1 sequence pathogenic variants. Results: The sensitivity of the test to detect spinal muscular atrophy (SMA) carriers with one copy of SMN1 was 100% (95% confidence interval (CI): 95.9–100%; n = 90) and specificity was 99.6% (95% CI: 99.4–99.7%; n = 6,648). Detection of the g.27134T>G SNP by NGS was 100% concordant with an restriction fragment-length polymorphism method ( n = 493). Ten single-nucleotide variants in SMN1 were detectable by NGS and confirmed by gene-specific amplicon-based sequencing. This comprehensive approach yielded SMA carrier detection rates of 90.3–95.0% in five ethnic groups studied. Conclusion: We have developed a novel, comprehensive SMN1 copy-number and sequence variant analysis method by NGS that demonstrated improved SMA carrier detection rates across the entire population examined. Genet Med advance online publication 19 January 2017

Background Exome sequencing (ES) has been successfully applied in clinical detection of single nucleotide variants (SNVs) and small indels. However, identification of copy number variants (CNVs) using ES data remains challenging. The purpose of this study is to understand the contribution of CNVs and copy neutral runs of homozygosity (ROH) in molecular diagnosis of patients referred for ES. Methods In a cohort of 11,020 consecutive ES patients, an Illumina SNP array analysis interrogating mostly coding SNPs was performed as a quality control (QC) measurement and for CNV/ROH detection. Among these patients, clinical chromosomal microarray analysis (CMA) was performed at Baylor Genetics (BG) on 3229 patients, either before, concurrently, or after ES. We retrospectively analyzed the findings from CMA and the QC array. Results The QC array can detect ~ 70% of pathogenic/likely pathogenic CNVs (PCNVs) detectable by CMA. Out of the 11,020 ES cases, the QC array identified PCNVs in 327 patients and uniparental disomy (UPD) disorder-related ROH in 10 patients. The overall PCNV/UPD detection rate was 5.9% in the 3229 ES patients who also had CMA at BG; PCNV/UPD detection rate was higher in concurrent ES and CMA than in ES with prior CMA (7.2% vs 4.6%). The PCNVs/UPD contributed to the molecular diagnoses in 17.4% (189/1089) of molecularly diagnosed ES cases with CMA and were estimated to contribute in 10.6% of all molecularly diagnosed ES cases. Dual diagnoses with both PCNVs and SNVs were detected in 38 patients. PCNVs affecting single recessive disorder genes in a compound heterozygous state with SNVs were detected in 4 patients, and homozygous deletions (mostly exonic deletions) were detected in 17 patients. A higher PCNV detection rate was observed for patients with syndromic phenotypes and/or cardiovascular abnormalities. Conclusions Our clinical genomics study demonstrates that detection of PCNV/UPD through the QC array or CMA increases ES diagnostic rate, provides more precise molecular diagnosis for dominant as well as recessive traits, and enables more complete genetic diagnoses in patients with dual or multiple molecular diagnoses. Concurrent ES and CMA using an array with exonic coverage for disease genes enables most effective detection of both CNVs and SNVs and therefore is recommended especially in time-sensitive clinical situations.

Whole-exome sequencing can be used to obtain a genetic diagnosis for patients thought to be affected by a genetic disease. Here, investigators providing a sequencing service to physicians report the results for the first 250 consecutive patients who underwent analysis. Mendelian diseases are considered to be rare, yet genetic disorders are estimated to occur at a rate of 40 to 82 per 1000 live births. 1 Epidemiologic studies show that if all congenital anomalies are considered as part of the genetic load, then approximately 8% of persons are identified as having a genetic disorder before reaching adulthood. 2 Collectively, rare genetic disorders affect substantial numbers of persons. Many patients with genetic diseases are not given a specific diagnosis. The standard of practice involves the recognition of specific phenotypic or radiographic features or biopsy findings in addition to the analysis of metabolites, genomic . . .

The artwork of many of the school's Communications/Media students are displayed on the walls of the Campus Center Art Gallery making up the annual exhibit. Visions is a student honor show designed to recognize the achievements of students in the areas of graphic design, photography, computer graphic design, film, video and technical communications.

Math problems are adding money to children's cancer research and increasing the scholastic skills of students. Seventh- , eighth- and ninth-grade students at Narragansett Regional High School in Baldwinville are extending their mathematics skills beyond the classroom while raising money for cancer research. The St. Jude Children Research Hospital's Math-A-Thon program has attracted nearly 70 NRHS students. Each student will gather sponsors and complete a \"math-fun\" workbook, containing 200 math activities geared toward the math curriculum taught in each corresponding grade.

WESTMINSTER - Eight Camp Fire Girls here have found a way to convert seemingly useless cancelled postage stamps into objects of value that help others. Under the direction of Jill E. Connors and Joanne Morse, parent/volunteer leaders and former Camp Fire Girls, the group has collected 2,570 cancelled postage stamps since October 1994, far exceeding their original goal of 500. This project will enable the girls to enter the 22nd Annual Community Service Campaign of Colgate's Youth for America, with prizes ranging from $100 to $1,000.