On The Spot e-News
Volume 3, Issue 1 | January 2008
In this issue:
- Signature Microarray Covers Regions of the Genome Associated with Autism
- Microdeletion Syndrome Discovered by Signature Profiled in New York Times
- SignatureChip Used to Characterize Complex Chromosomal Aberrations in Recurrent Tumor
- Genoglyphix to Offer New Microarray
Signature Microarray Covers Regions of the Genome Associated with Autism
Signature Genomic Laboratories’ flagship microarray, the SignatureChip Whole Genome™ (SignatureChipWG™), covers a region of the human genome that was recently associated with autism.
A story in the New York Times published Jan. 10 reports on a study by researchers from the Autism Consortium showing approximately 1% of individuals with autism have missing a small segment of the short arm of one of their chromosomes 16. The study, originally published in the New England Journal of Medicine, corroborates findings published last month in the scientific journal Human Molecular Genetics, in which researchers from the University of Chicago and Roswell Park Cancer Institute in Buffalo, N.Y. identified similar deletions in two children with autism.
The SignatureChipWG, the latest version of Signature’s proprietary SignatureChip microarray, has extensive coverage of this region of chromosome 16. Since the introduction of the SignatureChipWG in November, Signature has recorded seven losses and four gains of the autism region among 1,283 cases tested.
In addition to the region recently reported, the SignatureChipWG covers over 30 regions of the genome associated with autism.
Microdeletion Syndrome Discovered by Signature Profiled in New York Times
Two children with a genomic disorder first reported by researchers at Signature Genomic Laboratories, LLC were recently profiled by the New York Times.
The two children were among four individuals referred to Signature for genetic testing who were diagnosed, using the SignatureChip targeted microarray, with a submicroscopic deletion on the short arm of chromosome 16. The syndrome, the clinical features of which include mental retardation, distinct facial features, short stature, heart defects and feeding difficulties, was first decribed in the scientific journal Nature Genetics in an article titled "Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-p12.2." The Times story describes how the girls’ families, both of which reside in Kentucky, met following publication of the research paper; for both families, it was the first time they had met another individual with this rare chromosome abnormality.
"I think this is the kind of story we will hear about more often as microarray technology becomes more widely used," said Dr. Lisa G. Shaffer, PhD, Chief Executive Officer and Director of Signature Genomic Laboratories. "Some of these families have been searching for years for what is causing their children’s health problems, and microarrays are finally able to give them answers.’
SignatureChip Used to Characterize Complex Chromosomal Aberrations in Recurrent Tumor
A recent study demonstrates the utility of array CGH in the characterization of previously identified chromosomal abnormalities.
In the study, published in Cancer Genetics and Cytogenetics, Woo and colleagues analyzed by conventional cytogenetic analysis a primary and a recurrent tumor and by microarray analysis recurrent tumor DNA from a 62-year-old male. Cytogenetic analysis showed that in both tumors all 20 metaphases examined were abnormal. Fifteen of 20 cells from the recurrent tumor showed the same karyotype as the initial tumor, 42,XY,der(1)t(1;?)(p12;?),-6,der(12;15)(q10;q10),-18,-22. The remaining cells showed, in addition to the original karyotype, +15 in three cells and +der(1)t(1;?) and +i(1)(q10) in one cell each, suggesting tumor progression. Micoarray analysis performed by Signature Genomic Laboratories using the SignatureChip® on recurrent tumor DNA cells identified the five complex abnormalities detected by G-banding, but also revealed a terminal duplication of the short arm of chromosome 6. Because array CGH can simultaneously analyze all tumor cells, it clarified the cytogenetic results and showed a more complex rearrangement of chromosome 6. Although meningiomas are benign tumors, a complex karyotype suggests an aggressive phenotype, which affects tumor prognosis.
Genoglyphix to Offer New Microarray
Signature announces the imminent release to its Genoglyphix customers of a new microarray for research applications.
Available for purchase by cytogenetic laboratories for research use in the first quarter of 2008, the SignatureSelectV2.0 chip offers increased resolution over our current research-use-only chip, the SignatureSelect. In its most innovative approach to date, Signature has anchored every BAC contig onto one or more genes of known function in important developmental pathways. The result is whole-genome coverage with an average gap of 1.6 megabases (Mb) across the genome and a resolution of 80 kilobases (kb). In addition, every abnormality detected by the SignatureSelectV2.0 can be visualized by FISH, because each clone has been uniquely selected and rigorously evaluated by FISH to ensure it represents the correct region of the genome. FISH visualization is essential for providing accurate information about the nature and causative mechanism of the chromosome alteration. Used in conjunction with our Genoglyphix service, the SignatureSelectV2.0 is the most comprehensive microarray available for the investigation of chromosomal abnormalities in patients with developmental delay and congenital anomalies.
Call Signature Genomic Laboratories at 1.877.GGXChip (1.877.449.2447) or e-mail info@genoglyphix.com to find out how your laboratory can benefit from Signature’s Genoglyphix service, or read our frequently asked questions.