Copyright © 2008 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 82, Issue 3, 763-771, 14 February 2008
doi:10.1016/j.ajhg.2007.12.011
Report
Carl E.G. Bruder1,
,
, Arkadiusz Piotrowski1, Antoinet A.C.J. Gijsbers2, 3, Robin Andersson4, Stephen Erickson5, Teresita Diaz de Ståhl6, Uwe Menzel6, Johanna Sandgren7, Desiree von Tell1, Andrzej Poplawski1, Michael Crowley1, Chiquito Crasto1, E. Christopher Partridge1, Hemant Tiwari5, David B. Allison1, 5, Jan Komorowski4, Gert-Jan B. van Ommen2, 3, Dorret I. Boomsma8, Nancy L. Pedersen9, Johan T. den Dunnen2, 3, Karin Wirdefeldt9 and Jan P. Dumanski1, 6
1 Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
2 Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC), 2300 RC Leiden, The Netherlands
3 Center for Medical Systems Biology, 2300 RA Leiden, The Netherlands
4 Linnaeus Centre for Bioinformatics, Uppsala University, SE-75124 Uppsala, Sweden
5 Section on Statistical Genetics, Department of Biostatistics, University of Alabama at Birmingham, Ryals Public Health Building, Suite 327, Birmingham, Alabama 35294-0022, USA
6 Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
7 Department of Surgical Sciences, Uppsala Academic Hospital, Uppsala University, SE-751 85 Uppsala, Sweden
8 Department of Biological Psychology, VU University, Van der Boechorststraat 1, 1081 BT Amsterdam, The Netherlands
9 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
Corresponding authorAbstract
The exploration of copy-number variation (CNV), notably of somatic cells, is an understudied aspect of genome biology. Any differences in the genetic makeup between twins derived from the same zygote represent an irrefutable example of somatic mosaicism. We studied 19 pairs of monozygotic twins with either concordant or discordant phenotype by using two platforms for genome-wide CNV analyses and showed that CNVs exist within pairs in both groups. These findings have an impact on our views of genotypic and phenotypic diversity in monozygotic twins and suggest that CNV analysis in phenotypically discordant monozygotic twins may provide a powerful tool for identifying disease-predisposition loci. Our results also imply that caution should be exercised when interpreting disease causality of de novo CNVs found in patients based on analysis of a single tissue in routine disease-related DNA diagnostics.
| Structural Variation of Chromosomes in Autism Spectrum Disorder The American Journal of Human Genetics, Volume 82, Issue 2, 8 February 2008, Pages 477-488 Christian R. Marshall, Abdul Noor, John B. Vincent, Anath C. Lionel, Lars Feuk, Jennifer Skaug, Mary Shago, Rainald Moessner, Dalila Pinto, Yan Ren, Bhooma Thiruvahindrapduram, Andreas Fiebig, Stefan Schreiber, Jan Friedman, Cees E.J. Ketelaars, Yvonne J. Vos, Can Ficicioglu, Susan Kirkpatrick, Rob Nicolson, Leon Sloman, Anne Summers, Clare A. Gibbons, Ahmad Teebi, David Chitayat, Rosanna Weksberg, Ann Thompson, Cathy Vardy, Vicki Crosbie, Sandra Luscombe, Rebecca Baatjes, Lonnie Zwaigenbaum, Wendy Roberts, Bridget Fernandez, Peter Szatmari and Stephen W. Scherer Abstract Structural variation (copy number variation [CNV] including deletion and duplication, translocation, inversion) of chromosomes has been identified in some individuals with autism spectrum disorder (ASD), but the full etiologic role is unknown. We performed genome-wide assessment for structural abnormalities in 427 unrelated ASD cases via single-nucleotide polymorphism microarrays and karyotyping. With microarrays, we discovered 277 unbalanced CNVs in 44% of ASD families not present in 500 controls (and re-examined in another 1152 controls). Karyotyping detected additional balanced changes. Although most variants were inherited, we found a total of 27 cases with de novo alterations, and in three (11%) of these individuals, two or more new variants were observed. De novo CNVs were found in ∼7% and ∼2% of idiopathic families having one child, or two or more ASD siblings, respectively. We also detected 13 loci with recurrent/overlapping CNV in unrelated cases, and at these sites, deletions and duplications affecting the same gene(s) in different individuals and sometimes in asymptomatic carriers were also found. Notwithstanding complexities, our results further implicate the SHANK3-NLGN4-NRXN1 postsynaptic density genes and also identify novel loci at DPP6-DPP10-PCDH9 (synapse complex), ANKRD11, DPYD, PTCHD1, 15q24, among others, for a role in ASD susceptibility. Our most compelling result discovered CNV at 16p11.2 (p = 0.002) (with characteristics of a genomic disorder) at ∼1% frequency. Some of the ASD regions were also common to mental retardation loci. Structural variants were found in sufficiently high frequency influencing ASD to suggest that cytogenetic and microarray analyses be considered in routine clinical workup. Abstract | | |
| Copy-Number Variations Measured by Single-Nucleotide–Polymorphism Oligonucleotide Arrays in Patients with Mental Retardation The American Journal of Human Genetics, Volume 81, Issue 4, 1 October 2007, Pages 768-779 Janine Wagenstaller, Stephanie Spranger, Bettina Lorenz-Depiereux, Bernd Kazmierczak, Michaela Nathrath, Dagmar Wahl, Babett Heye, Dieter Gläser, Volkmar Liebscher, Thomas Meitinger and Tim M. Strom Abstract Whole-genome analysis using high-density single-nucleotide–polymorphism oligonucleotide arrays allows identification of microdeletions, microduplications, and uniparental disomies. We studied 67 children with unexplained mental retardation with normal karyotypes, as assessed by G-banded chromosome analyses. Their DNAs were analyzed with Affymetrix 100K arrays. We detected 11 copy-number variations that most likely are causative of mental retardation, because they either arose de novo (9 cases) and/or overlapped with known microdeletions (2 cases). The eight deletions and three duplications varied in size from 200 kb to 7.5 Mb. Of the 11 copy-number variations, 5 were flanked by low-copy repeats. Two of those, on chromosomes 15q25.2 and Xp22.31, have not been described before and have a high probability of being causative of new deletion and duplication syndromes, respectively. In one patient, we found a deletion affecting only a single gene, MBD5, which codes for the methyl-CpG-binding domain protein 5. In addition to the 67 children, we investigated 4 mentally retarded children with apparent balanced translocations and detected four deletions at breakpoint regions ranging in size from 1.1 to 14 Mb. Abstract | | |