Swift: primary data analysis for the Illumina Solexa sequencing platform

Motivation: Primary data analysis methods are of critical importance in second generation DNA sequencing. Improved methods have the potential to increase yield and reduce the error rates. Openly documented analysis tools enable the user to understand the primary data, this is important for the optimization and validity of their scientific work

Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.

We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities

String matching in DNA sequences : implications for short read sequencing and repeat visualisation

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Thermal equivalence of DNA duplexes without calculation of melting temperature

The common key to nearly all processes involving DNA is the hybridization and melting of the double helix: from transmission of genetic information and RNA transcription, to polymerase chain reaction and DNA microarray analysis, DNA mechanical nanodevices and DNA computing. Selecting DNA sequences with similar melting temperatures is essential for many applications in biotechnology. We show that instead of calculating these temperatures, a single parameter can be derived from a statistical-mechanics model that conveniently represents the thermodynamic equivalence of DNA sequences. This parameter is shown to order experimental melting temperatures correctly, is much more readily obtained than the melting temperature, and is easier to handle than the numerous parameters of empirical regression models

A) Number of fragments 〈〉 found the selected target sequence Influenza (NCBI∶CY000076) that are correctly identified as a function of probe length

The average standard error is 0.23% and was consistent across all the data points. b) The average number of probes

Reassembled contigs longer than 200 nt in the 81 090 nt of the BRCA1 gene

<p><b>Copyright information:</b></p><p>Taken from "An analysis of the feasibility of short read sequencing"</p><p>Nucleic Acids Research 2005;33(19):e171-e171.</p><p>Published online 7 Nov 2005</p><p>PMCID:PMC1278949.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> <p>http://dx.crossref.org/10.1093%2Fnar%2Fgni170</p> Reassembly was simulated from 25, 50 and 100 nt reads covering the whole of chromosome 17. Reassembled contigs are shown in alternating black and grey. Contigs maybe next to each other, or overlapping slightly without an unambiguous overlap existing between the contigs

Percentage of unique sub-sequences (U) for varying read length (l), the solid line shows uniqueness in the whole human genome, the dashed line shows uniqueness in human chromosome 1

<p><b>Copyright information:</b></p><p>Taken from "An analysis of the feasibility of short read sequencing"</p><p>Nucleic Acids Research 2005;33(19):e171-e171.</p><p>Published online 7 Nov 2005</p><p>PMCID:PMC1278949.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> (a) Percentage of unique sub-sequences (U) for varying read length (l), the solid line shows uniqueness in the whole human genome, the dashed line shows uniqueness in human chromosome 1. (b) Percentage of human chromosome 1 covered by contigs greater than a threshold length as a function of read length. The horizontal axis starts at 18 nt, due to the limitations of reassembly below this length