ISB Family Genomics papers
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ISB Family Genomics papers
A collection of papers published by the Family Genomics team at the Institute for Systems Biology
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Clinical applications of sequencing take center stage

A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013.

This year's Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of 'next generation' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existing technologies continued to improve following the now expected exponential curve. Although applications ranged widely, there was a strong emphasis on clinical diagnosis.

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Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

We analyzed the whole genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in 99.999% accuracy), and identify very rare single nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of ~1.1 x 10-8 per position per haploid genome. Both offspring in this family have two recessive disorders—Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the unique value of complete genome sequencing in families.

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KAVIAR: an accessible system for testing SNV novelty

Summary: With the rapidly expanding availability of data from personal genomes, exomes and transcriptomes, medical researchers will frequently need to test whether observed genomic variants are novel or known. This task requires downloading and handling large and diverse data sets from a variety of sources, and processing them with bioinformatics tools and pipelines. Alternatively, researchers can upload data to online tools, which may conflict with privacy requirements. We present here Kaviar, a tool that greatly simplifies the assessment of novel variants. Kaviar includes a) an integrated and growing database of genomic variation from diverse sources, including over 55 million variants from personal genomes, family genomes, transcriptomes, SNP databases and population surveys, and b) software for querying the database efficiently.

Availability: Kaviar is programmed in Perl and offered free of charge as Open Source Software. Kaviar may be used online, as a programmatic web service, or downloaded for local use, from http://db.systemsbiology.net/kaviar. The database is also provided.

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F1000Research Article: Low budget analysis of Direct-To-Consumer genomic testing familial data.

Read the latest article version by Gustavo Glusman, Mike Cariaso, Rafael Jimenez, Daniel Swan, Bastian Greshake, Jong Bhak, Darren W Logan, Manuel Corpas, at F1000Research.
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Chromosomal Haplotypes by Genetic Phasing of Human Families

Assignment of alleles to haplotypes for nearly all the variants on all chromosomes can be performed by genetic analysis of a nuclear family with three or more children. Whole-genome sequence data enable deterministic phasing of nearly all sequenced alleles by permitting assignment of recombinations to precise chromosomal positions and specific meioses. We demonstrate this process of genetic phasing on two families each with four children. We generate haplotypes for all of the children and their parents; these haplotypes span all genotyped positions, including rare variants. Misassignments of phase between variants (switch errors) are nearly absent. Our algorithm can also produce multimegabase haplotypes for nuclear families with just two children and can handle families with missing individuals. We implement our algorithm in a suite of software scripts (Haploscribe). Haplotypes and family genome sequences will become increasingly important for personalized medicine and for fundamental biology.

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