Universität zu Köln

Altmueller, Janine, Motameny, Susanne, Becker, Christian, Thiele, Holger, Chatterjee, Sreyoshi, Wollnik, Bernd and Nuernberg, Peter (2016). A systematic comparison of two new releases of exome sequencing products: the aim of use determines the choice of product. Biol. Chem., 397 (8). S. 791 - 802. BERLIN: WALTER DE GRUYTER GMBH. ISSN 1437-4315

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Abstract

We received early access to the newest releases of exome sequencing products, namely Agilent SureSelect v6 (Agilent, Santa Clara, CA, USA) and NimbleGen MedExome (Roche NimbleGen, Basel, Switzerland), and we conducted whole exome sequencing (WES) of several DNA samples with each of these products in order to assess their performance. Here, we provide a detailed evaluation of the original, normalized (with respect to the different target sizes), and trimmed data sets and compare them in terms of the amount of duplicates, the reads on target, and the enrichment evenness. In addition to these general statistics, we performed a detailed analysis of the frequently mutated and newly described genes found in 'The Deciphering Developmental Disorders Study' published very recently (Fitzgerald, T.W., Gerety, S.S., Jones, W.D., van Kogelenberg, M., King, D.A., McRae, J., Morley, K.I., Parthiban, V., Al-Turki, S., Ambridge, K., et al. (2015). Large-scale discovery of novel genetic causes of developmental disorders. Nature 519, 223-228.). In our comparison, the Agilent v6 exome performs better than the NimbleGen's MedExome both in terms of efficiency and evenness of coverage distribution. With its larger target size, it is also more comprehensive, and therefore the better choice in research projects that aim to identify novel disease-associated genes. In contrast, if the exomes are mainly used in a diagnostic setting, we see advantages for the new NimbleGen MedExome. We find a superior coverage here in those genes of high clinical relevance that likely allows for a better detection of relevant, disease-causing mutations.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Altmueller, Janine UNSPECIFIED UNSPECIFIED UNSPECIFIED Motameny, Susanne UNSPECIFIED UNSPECIFIED UNSPECIFIED Becker, Christian UNSPECIFIED UNSPECIFIED UNSPECIFIED Thiele, Holger UNSPECIFIED UNSPECIFIED UNSPECIFIED Chatterjee, Sreyoshi UNSPECIFIED UNSPECIFIED UNSPECIFIED Wollnik, Bernd UNSPECIFIED UNSPECIFIED UNSPECIFIED Nuernberg, Peter UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-268528
DOI:	10.1515/hsz-2015-0300
Journal or Publication Title:	Biol. Chem.
Volume:	397
Number:	8
Page Range:	S. 791 - 802
Date:	2016
Publisher:	WALTER DE GRUYTER GMBH
Place of Publication:	BERLIN
ISSN:	1437-4315
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language PERFORMANCE; CONTAMINATION Multiple languages Biochemistry & Molecular Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/26852