The International Journal of Neuropsychopharmacology

Reviews

Making sense of deep sequencing

D. Goldmana1 and K. Domschkea2 c1

a1 Laboratory of Neurogenetics, NIAAA, NIH, Rockville, MD, USA

a2 Department of Psychiatry, University of Wuerzburg, Wuerzburg, Germany

Abstract

This review, the first of an occasional series, tries to make sense of the concepts and uses of deep sequencing of polynucleic acids (DNA and RNA). Deep sequencing, synonymous with next-generation sequencing, high-throughput sequencing and massively parallel sequencing, includes whole genome sequencing but is more often and diversely applied to specific parts of the genome captured in different ways, for example the highly expressed portion of the genome known as the exome and portions of the genome that are epigenetically marked either by DNA methylation, the binding of proteins including histones, or that are in different configurations and thus more or less accessible to enzymes that cleave DNA. Deep sequencing of RNA (RNASeq) reverse-transcribed to complementary DNA is invaluable for measuring RNA expression and detecting changes in RNA structure. Important concepts in deep sequencing include the length and depth of sequence reads, mapping and assembly of reads, sequencing error, haplotypes, and the propensity of deep sequencing, as with other types of ‘big data’, to generate large numbers of errors, requiring monitoring for methodologic biases and strategies for replication and validation. Deep sequencing yields a unique genetic fingerprint that can be used to identify a person, and a trove of predictors of genetic medical diseases. Deep sequencing to identify epigenetic events including changes in DNA methylation and RNA expression can reveal the history and impact of environmental exposures. Because of the power of sequencing to identify and deliver biomedically significant information about a person and their blood relatives, it creates ethical dilemmas and practical challenges in research and clinical care, for example the decision and procedures to report incidental findings that will increasingly and frequently be discovered.

(Received March 08 2014)

(Reviewed March 21 2014)

(Revised April 17 2014)

(Accepted April 18 2014)

(Online publication June 13 2014)

Key words

  • ChipSeq;
  • exome;
  • methylome;
  • next-generation sequencing;
  • RNASeq

Correspondence

c1 Address for correspondence: Katharina Domschke, Department of Psychiatry, University of Wuerzburg, Fuechsleinstrasse 15, D-97080 Wuerzburg, Germany. Tel.: ++49-931-20177100 Fax: ++49-931-20177109 Email: Domschke_K@ukw.de