Copyright © 2008 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 82, Issue 5, 1171-1177, 17 April 2008
doi:10.1016/j.ajhg.2008.03.005
Report
Jeff M. Milunsky1, 2, 3,
,
, Tom A. Maher1, Geping Zhao1, Amy E. Roberts4, Heather J. Stalker5, Roberto T. Zori5, Michelle N. Burch5, Michele Clemens6, John B. Mulliken7, Rosemarie Smith8 and Angela E. Lin9
1 Center for Human Genetics, Boston University School of Medicine, Boston, MA 02118-2526, USA
2 Department of Pediatrics, Boston University School of Medicine, Boston, MA 02118-2526, USA
3 Department of Genetics and Genomics, Boston University School of Medicine, Boston, MA 02118-2526, USA
4 Department of Cardiology, Children's Hospital, Boston, MA 02114, USA
5 Division of Genetics, Raymond C. Philips Unit, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
6 Department of Genetics, Magee-Womens Hospital of UPMC, Pittsburgh, PA, USA
7 Department of Plastic Surgery, Children's Hospital, Boston, MA 02118-2526, USA
8 Division of Genetics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, ME, USA
9 Genetics Unit, MassGeneral Hospital for Children, Simches Research Building 2222, 185 Cambridge Avenue, Boston, MA 02114, USA
Corresponding authorAbstract
Branchio-oculo-facial syndrome (BOFS) is a rare autosomal-dominant cleft palate-craniofacial disorder with variable expressivity. The major features include cutaneous anomalies (cervical, infra- and/or supra-auricular defects, often with dermal thymus), ocular anomalies, characteristic facial appearance (malformed pinnae, oral clefts), and, less commonly, renal and ectodermal (dental and hair) anomalies. The molecular basis for this disorder is heretofore unknown. We detected a 3.2 Mb deletion by 500K SNP microarray in an affected mother and son with BOFS at chromosome 6p24.3. Candidate genes in this region were selected for sequencing on the basis of their expression patterns and involvement in developmental pathways associated with the clinical findings of BOFS. Four additional BOFS patients were found to have de novo missense mutations in the highly conserved exons 4 and 5 (basic region of the DNA binding domain) of the TFAP2A gene in the candidate deleted region. We conclude BOFS is caused by mutations involving TFAP2A. More patients need to be studied to determine possible genetic heterogeneity and to establish whether there are genotype-phenotype correlations.
| Genomewide Scan for Nonsyndromic Cleft Lip and Palate in Multigenerational Indian Families Reveals Significant Evidence of Linkage at 13q33.1-34 The American Journal of Human Genetics, Volume 79, Issue 3, 1 September 2006, Pages 580-585 Uppala Radhakrishna, Uppala Ratnamala, Mathew Gaines, Soraya Beiraghi, David Hutchings, Jeffrey Golla, Syed A. Husain, Prakash S. Gambhir, Jayesh J. Sheth, Frenny J. Sheth, Ghati K. Chetan, Mohammed Naveed, Jitendra V. Solanki, Uday C. Patel, Dilipkumar C. Master, Rafiq Memon, Gregory S. Antonarakis, Stylianos E. Antonarakis and Swapan K. Nath Abstract Nonsyndromic cleft lip with or without cleft palate (CL-P) is a common congenital anomaly with incidence ranging from 1 in 300 to 1 in 2,500 live births. We analyzed two Indian pedigrees (UR017 and UR019) with isolated, nonsyndromic CL-P, in which the anomaly segregates as an autosomal dominant trait. The phenotype was variable, ranging from unilateral to bilateral CL-P. A genomewide linkage scan that used ∼10,000 SNPs was performed. Nonparametric linkage (NPL) analysis identified 11 genomic regions (NPL>3.5; P<.005) that could potentially harbor CL-P susceptibility variations. Among those, the most significant evidence was for chromosome 13q33.1-34 at marker rs1830756 (NPL=5.57; P=.00024). This was also supported by parametric linkage; MOD score (LOD scores maximized over genetic model parameters) analysis favored an autosomal dominant model. The maximum LOD score was 4.45, and heterogeneity LOD was 4.45 (α=100%). Haplotype analysis with informative crossovers enabled the mapping of the CL-P locus to a region of ∼20.17 cM (7.42 Mb) between SNPs rs951095 and rs726455. Thus, we have identified a novel genomic region on 13q33.1-34 that harbors a high-risk variant for CL-P in these Indian families. Abstract | | |
| Orofacial Cleft Risk Is Increased with Maternal Smoking and Specific Detoxification-Gene Variants The American Journal of Human Genetics, Volume 80, Issue 1, 1 January 2007, Pages 76-90 Min Shi, Kaare Christensen, Clarice R. Weinberg, Paul Romitti, Lise Bathum, Anthony Lozada, Richard W. Morris, Michael Lovett and Jeffrey C. Murray Abstract Maternal smoking is a recognized risk factor for orofacial clefts. Maternal or fetal pharmacogenetic variants are plausible modulators of this risk. In this work, we studied 5,427 DNA samples, including 1,244 from subjects in Denmark and Iowa with facial clefting and 4,183 from parents, siblings, or unrelated population controls. We examined 25 single-nucleotide polymorphisms in 16 genes in pathways for detoxification of components of cigarette smoke, to look for evidence of gene-environment interactions. For genes identified as related to oral clefting, we studied gene-expression profiles in fetal development in the relevant tissues and time intervals. Maternal smoking was a significant risk factor for clefting and showed dosage effects, in both the Danish and Iowan data. Suggestive effects of variants in the fetal NAT2 and CYP1A1 genes were observed in both the Iowan and the Danish participants. In an expanded case set, NAT2 continued to show significant overtransmission of an allele to the fetus, with a final P value of .00003. There was an interaction between maternal smoking and fetal inheritance of a GSTT1-null deletion, seen in both the Danish (P=.03) and Iowan (P=.002) studies, with a Fisher’s combined P value of <.001, which remained significant after correction for multiple comparisons. Gene-expression analysis demonstrated expression of GSTT1 in human embryonic craniofacial tissues during the relevant developmental interval. This study benefited from two large samples, involving independent populations, that provided substantial power and a framework for future studies that could identify a susceptible population for preventive health care. Abstract | | |
| Characterization of Apparently Balanced Chromosomal Rearrangements from the Developmental Genome Anatomy Project The American Journal of Human Genetics, Volume 82, Issue 3, 3 March 2008, Pages 712-722 Anne W. Higgins, Fowzan S. Alkuraya, Amy F. Bosco, Kerry K. Brown, Gail A.P. Bruns, Diana J. Donovan, Robert Eisenman, Yanli Fan, Chantal G. Farra, Heather L. Ferguson, James F. Gusella, David J. Harris, Steven R. Herrick, Chantal Kelly, Hyung-Goo Kim, Shotaro Kishikawa, Bruce R. Korf, Shashikant Kulkarni, Eric Lally, Natalia T. Leach, Emma Lemyre, Janine Lewis, Azra H. Ligon, Weining Lu, Richard L. Maas, Marcy E. MacDonald, Steven D.P. Moore, Roxanna E. Peters, Bradley J. Quade, Fabiola Quintero-Rivera, Irfan Saadi, Yiping Shen, Jay Shendure, Robin E. Williamson and Cynthia C. Morton Abstract Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation. Abstract | | |