Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

Abstract

Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, with several others anticipated to become available shortly. The previously unimaginable scale and economy of these methods, coupled with their enthusiastic uptake by the scientific community and the potential for further improvements in accuracy and read length, suggest that these technologies are destined to make a huge and ongoing impact upon genomic and post-genomic biology. However, like the analysis of microarray data and the assembly and annotation of complete genome sequences from conventional sequencing data, the management and analysis of next-generation sequencing data requires (and indeed has already driven) the development of informatics tools able to assemble, map, and interpret huge quantities of relatively or extremely short nucleotide sequence data. Here we provide a broad overview of bioinformatics approaches that have been introduced for several genomics and functional genomics applications of next-generation sequencing.

Mammary-digital-nail (MDN) syndrome: a novel phenotype maps to human chromosome 22q12.3–13.1

“…Patient IV 25 , the first affected individual to be identified, was referred for breast reduction surgery due to premenarche massive breast enlargement, as we previously reported. 2 Her immediate and extended family lives in an isolated village of 13 000 Druze residents in northern Israel.…”

“…In patients IV 25 , III 10 , IV 19 , and IV 20 ( Figure 2) breasts enlarged dramatically, reaching enormous proportion during a 3-month period before and shortly after menarche. 2 Of note, female patient III 9 , who died at the age of 3 years, well before her premenarche time, presented with ODP only.…”

“…10 Two physicians conducted complete physical examinations and detailed interviews of the medical and family history of the 41 members of the kindred who agreed to participate in the study. Patients III 19 , IV 20 , IV 25 , and IV 28 ( Figure 2) underwent X-rays of hands, feet, and long bones.…”

“…We compared cDNA isolated from skin and/or mammary tissues of four affected family members (two males and two females), IV 19 , IV 25 , IV 21 , and IV 28 ( Figure 2) to that of five unrelated unaffected individuals (three males and two females). Breast tissue was removed solely from females.…”

Gene dynamics of toll-like receptor 4 through a population bottleneck in an insular population of water voles (Arvicola amphibius)

“…However, the MHC represents only a small portion of the immunogenome as well as the broader adaptive fraction of the overall genome. The advent of post-genomics technologies and analyses has greatly enhanced the potential to identify and target key genome regions outside the MHC that represent functional genetic variation of ecological relevance (Blackwell 2001;Piertney and Webster 2008;Horner et al 2010). This is an essential step forward, given that there are many other non-MHC immune function genes that play pivotal roles in the vertebrate immune system (Acevedo-Whitehouse and Cunningham 2006).…”