Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes

Francesco Lescai, Silvia Bonfiglio, Chiara Bacchelli, Estelle Chanudet, Aoife Waters, Sanjay M. Sisodiya, Dalia Kasperavičiute, Julie Williams, Denise Harold, John Hardy, Robert Kleta, Sebahattin Cirak, Richard Williams, John C. Achermann, John Anderson, David Kelsell, Tom Vulliamy, Henry Houlden, Nicholas Wood, Una Sheerin & 10 others Gian Paolo Tonini, Donna Mackay, Khalid Hussain, Jane Sowden, Veronica Kinsler, Justyna Osinska, Tony Brooks, Mike Hubank, Philip Beales, Elia Stupka

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Recent advances in genomics technologies have spurred unprecedented efforts in genome and exome re-sequencing aiming to unravel the genetic component of rare and complex disorders. While in rare disorders this allowed the identification of novel causal genes, the missing heritability paradox in complex diseases remains so far elusive. Despite rapid advances of next-generation sequencing, both the technology and the analysis of the data it produces are in its infancy. At present there is abundant knowledge pertaining to the role of rare single nucleotide variants (SNVs) in rare disorders and of common SNVs in common disorders. Although the 1,000 genome project has clearly highlighted the prevalence of rare variants and more complex variants (e.g. insertions, deletions), their role in disease is as yet far from elucidated. We set out to analyse the properties of sequence variants identified in a comprehensive collection of exome re-sequencing studies performed on samples from patients affected by a broad range of complex and rare diseases (N = 173). Given the known potential for Loss of Function (LoF) variants to be false positive, we performed an extensive validation of the common, rare and private LoF variants identified, which indicated that most of the private and rare variants identified were indeed true, while common novel variants had a significantly higher false positive rate. Our results indicated a strong enrichment of very low-frequency insertion/deletion variants, so far under-investigated, which might be difficult to capture with low coverage and imputation approaches and for which most of study designs would be under-powered. These insertions and deletions might play a significant role in disease genetics, contributing specifically to the underlining rare and private variation predicted to be discovered through next generation sequencing.

Original languageEnglish
Article numbere51292
JournalPLoS One
Volume7
Issue number12
DOIs
Publication statusPublished - Dec 14 2012

Fingerprint

Exome
Nucleotides
nucleotides
Genome
Technology
application coverage
Inborn Genetic Diseases
genome
Genes
genetic disorders
infancy
Rare Diseases
Genomics
Sequence Analysis
data analysis
heritability
experimental design
genomics
genes
sampling

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Lescai, F., Bonfiglio, S., Bacchelli, C., Chanudet, E., Waters, A., Sisodiya, S. M., ... Stupka, E. (2012). Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes. PLoS One, 7(12), [e51292]. https://doi.org/10.1371/journal.pone.0051292

Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes. / Lescai, Francesco; Bonfiglio, Silvia; Bacchelli, Chiara; Chanudet, Estelle; Waters, Aoife; Sisodiya, Sanjay M.; Kasperavičiute, Dalia; Williams, Julie; Harold, Denise; Hardy, John; Kleta, Robert; Cirak, Sebahattin; Williams, Richard; Achermann, John C.; Anderson, John; Kelsell, David; Vulliamy, Tom; Houlden, Henry; Wood, Nicholas; Sheerin, Una; Tonini, Gian Paolo; Mackay, Donna; Hussain, Khalid; Sowden, Jane; Kinsler, Veronica; Osinska, Justyna; Brooks, Tony; Hubank, Mike; Beales, Philip; Stupka, Elia.

In: PLoS One, Vol. 7, No. 12, e51292, 14.12.2012.

Research output: Contribution to journalArticle

Lescai, F, Bonfiglio, S, Bacchelli, C, Chanudet, E, Waters, A, Sisodiya, SM, Kasperavičiute, D, Williams, J, Harold, D, Hardy, J, Kleta, R, Cirak, S, Williams, R, Achermann, JC, Anderson, J, Kelsell, D, Vulliamy, T, Houlden, H, Wood, N, Sheerin, U, Tonini, GP, Mackay, D, Hussain, K, Sowden, J, Kinsler, V, Osinska, J, Brooks, T, Hubank, M, Beales, P & Stupka, E 2012, 'Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes', PLoS One, vol. 7, no. 12, e51292. https://doi.org/10.1371/journal.pone.0051292
Lescai F, Bonfiglio S, Bacchelli C, Chanudet E, Waters A, Sisodiya SM et al. Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes. PLoS One. 2012 Dec 14;7(12). e51292. https://doi.org/10.1371/journal.pone.0051292
Lescai, Francesco ; Bonfiglio, Silvia ; Bacchelli, Chiara ; Chanudet, Estelle ; Waters, Aoife ; Sisodiya, Sanjay M. ; Kasperavičiute, Dalia ; Williams, Julie ; Harold, Denise ; Hardy, John ; Kleta, Robert ; Cirak, Sebahattin ; Williams, Richard ; Achermann, John C. ; Anderson, John ; Kelsell, David ; Vulliamy, Tom ; Houlden, Henry ; Wood, Nicholas ; Sheerin, Una ; Tonini, Gian Paolo ; Mackay, Donna ; Hussain, Khalid ; Sowden, Jane ; Kinsler, Veronica ; Osinska, Justyna ; Brooks, Tony ; Hubank, Mike ; Beales, Philip ; Stupka, Elia. / Characterisation and Validation of Insertions and Deletions in 173 Patient Exomes. In: PLoS One. 2012 ; Vol. 7, No. 12.
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