Developmental Genome Anatomy Project

Our Objective:

To identify apparently balanced chromosomal rearrangements in patients with multiple congenital anomalies and then to use these chromosomal rearrangements to map and identify genes that are disrupted or dysregulated in critical stages of human development and the influence pleine lune sur l’accouchement.

View a brief slide show that summarizes our project.

Project Highlights:

Project-wide: DGAP has analyzed the features of 77 breakpoints from 40 apparently balanced chromosomal rearrangements associated with developmental anomalies. In most case, multiple systems are involved. Unsuspected genomic imbalances and cryptic rearrangments were found, but less frequently than has been previously reported. Click the link to read our article in the Am J Hum Genet (2008; 82:712-722).

DGAP123 and DGAP200: Autism, a neurodevelopmental disorder of complex etiology, resulted from chromosomal rearrangement involving neurexin 1 (NRXN1) at 2p16.3 in two independent subjects [Am J Hum Genet, 2008; 82:199-207].

DGAP025: In humans and mice, chromodomain helicase DNA binding protein 2 (CHD2) disruption causes scoliosis [Am J Med Genet A, 2008; 146A:1117-1127].

DGAP089, DGAP104, DGAP174, and DGAP205: We describe five individuals who share phenotypically related CNS malformation and in some cases urinary tract defects, and also haploinsufficiency for the NFIA transcription factor gene due to chromosomal translocation or deletion [PLoS Genet, 2007; 3:830-843].

DGAP095: Diacylglycerol kinase delta (DGKD) disruption results in seizures in humans and mice [Am J Hum Genet, 2007; 80:792-799].

DGAP107: Disruption of ROBO2 is associated with urinary tract anomalies and confers risk of vesicoureteral reflux [Am J Hum Genet, 2007; 80:616-632].

DGAP016: N-myristoyltransferase (NMT2), which is highly expressed in the testes, was implicated as a cause of testicular hypoplasia [Am J Med Genet A, 2007; 143A:1796-1798].

DGAP090: Methylthioadenosine phosphorylase (MTAP) results in impaired hearing [Am J Med Genet A, 2007; 143A:1630-1639].

DGAP128: Synaptotagmin (SYT14) was associated with cerebral atrophy, seizures and developmental delay in a 12 year-old macrocephalic female [Am J Med Genet A, 2007; 143A:558-563].

DGAP151: SUMO1 haploinsufficiency and loss of post-translational sumoylation leads to cleft lip and palate [Science, 2006; 313:1751].

DGAP003: The translocation in DGAP003 identifies candidate loci for Zimmermann-Laband syndrome at 3p14.3 [Am J Med Genet A, 2007; 143A:2668-2674 and Am J Med Genet A, 2006; 143A:107-111].

DGAP011: Hypogonadotropic hypogonadism and cleft lip and palate can be caused by a balanced translocation producing haploinsufficiency for FGFR1 [Journal of Medical Genetics, 2005; 42:666-72)].

DGAP103: Constitutional rearrangement of the architectural factor HMGA2 results in a novel human phenotype including overgrowth and lipomas [American Journal of Human Genetics, 2005; 72:340-348].

Project-wide: DGAP contributes to the Research Article on Human chromosome 7: DNA sequence and biology in Science (2003; 300:767-72) [PDF] and its Supplemental On-line Material.

DGAP012: The breakpoint has been mapped to BAC CTD-3193o13 (GenBank AC010336 ) and near cosmid LLNLF-138h2 (GenBank AC008975). See the FISH image. This case was reported in Nature’s Genome issue on Feb. 15, 2001 [HTML][PDF].

Progress Summary:

DGAP Cases

Cases in database


Cases from the NIGMS Human Genetic Cell Repository

Cases collected by DGAP

FISH Mapping

Breakpoints FISH mapped

DGAP cases FISH mapped

Breakpoints mapped to a single BAC clone

DGAP cases with at least one breakpoint mapped to a single clone

Breakpoint Characterization

Breakpoints mapped to a single BAC clone

Macrodeletions detected (>600 kb)

Breakpoints within non-genic region

Breakpoints within conserverd non-genic region

Genes interrupted by a breakpoint

Breakpoints known to be within an intron

Breakpoints known to be within an exon

Breakpoint within 3’ untranslated region

Cases with at least one breakpoint sequenced

Breakpoints sequenced

Microdeletions at the breakpoint (ranging from 1 to 5,115 bp)

Duplications at the breakpoint

Insertions at the breakpoint

No sequence gain or loss from chromosome

Breakpoint within repetitive sequences





Fusion Products

Cases with predicted fusion proteins

Model Organisms



For assista nce in submitting a case, please contact:

Cynthia Morton, Ph.D.
(866) 772-5753 (toll-free)
(617) 525-4532 (direct)

To begin, select a strategy for searching the DGAP database:

I want to search:

by Cytogenetic Breakpoint Location
by Clinical Description (Free Text)
by Phenotype Category (List Box)
by DGAP Number

DGAP Investigators

Administrative Core

Cynthia C. Morton, Ph.D. – Principal Investigator

Clinical Core

David Harris, M.D. – Principal Investigator

Project 1: High Throughput Fish Mapping

Bradley J. Quade,M.D., Ph.D. – Principal Investigator

Project 2: Rapid Gene Discovery

James F. Gusella, Ph.D. – Principal Investigator

Project 3: Developmental Analysis Of Genes In Model Organisms

Richard L. Maas, M.D., Ph.D. – Principal Investigator

Internet Sites Related to DGAP

BAC Resources
The Clone Registry home page at the NCBI

The Human BAC Resource page at the NCBI

BACPAC Resources at the Children’s Hospital of Oakland Research Institute

NCBI Home Page

Cancer Genome Anatomy Project at NCI and NCBI

project Ensembl! at the Sanger Center and European Bioinformatics Institute

Human Genome Project BAC and Accession Maps at Washington University School of Medicine’s Genome Sequencing Center

Human Chromosome 7 Mapping and Sequencing page at the NHGRI

Dysmorphology Resources
Online Mendelian Inheritance in Man (OMIM) at NCBI and Johns Hopkins University

Information for Patients and Their Families

We thank you for your interest in the Developmental Genome Anatomy Project and our web site.
If you are interested in participating in our study, please contact us directly for further information.
Other web sites of interest to patients or families with congenital anomalies or chromosome abnormalities include:

Contact DGAP

For questions about… Please call or email… Project Title Phone number
Scientific matters Cynthia C. Morton, Ph.D. Principal Investigator (617) 525-4532
(866) 772-5753 [toll-free]
Study enrollment
Sample submission
Cynthia C. Morton, Ph.D.

Principal Investigator (617) 525-4532
(866) 772-5753 [toll-free]
Our website and database Bradley J. Quade, M.D., Ph.D. Project 1 Principal Investigator (617) 732-7980