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Exome sequencing: how to understand it
  1. M J Keogh1,2,
  2. D Daud3,
  3. P F Chinnery2
  1. 1James Cook University Hospital, Middlesbrough, UK
  2. 2Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
  3. 3Newcastle University, Newcastle, UK
  1. Correspondence to Prof P F Chinnery, Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle Upon Tyne NE1 3BZ, UK; p.f.chinnery{at}newcastle.ac.uk

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Introduction

Glossary of terms

Calling. The process of determining the DNA bases or regions in sequenced subjects that differ from the reference exome or genome.

Coverage. The number of times a single nucleotide in a sequence has been sequenced or read.

Exons. The protein coding regions.

Exome. The portion of the genome coding for proteins, ie, collectively, all of the exons.

Filtering. The process of removing mutations with the aim of leaving potential pathogenic variants only.

Genome. The complete DNA sequence of an organism.

Homozygosity mapping. A gene mapping method used in rare recessive disorders often in consanguineous families. It is based on the assumption that an allele responsible for disease is likely to occur from a common ancestor and looks for shared regions of inherited DNA between subjects.

Meiosis. Cell division that results in two daughter cells each with half the chromosome number of the parent cell. An essential step in the formation of the gametes.

Mendelian disorders. Genetic disorders that occur due to alterations or mutations in a single gene. Their pattern of inheritance can be recessive, dominant, or X-linked.

Next generation sequencing. Sequencing technology able to sequence thousands or millions of DNA regions at once—also referred to as second generation sequencing.

Penetrance. The proportion of individuals carrying a particular variant who also express an associated trait (phenotype).

Primer. A strand of DNA which serves as the starting point for DNA synthesis.

Single nucleotide polymorphism. A single variation of one base at a particular site of DNA.

Single nucleotide polymorphism array. A type of DNA microarray used to detect specific polymorphisms within a population and variation between genomes.

Third generation sequencing. Various methods of DNA sequencing which in general sequence single molecules of DNA, …

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