On The Spot e-News
Volume 2, Issue 3 | Fall 2007
In this issue:
- Detection of marker chromosomes by array CGH
- Signature Spotlight: Dicentric marker 22q
- Signature Profile: Blake Ballif, Director of Product Development and Research
The Detection of Marker Chromosomes by Array CGH
Although they are too small to be conclusively identified by conventional banding, small supernumerary marker chromosomes (sSMCs) have outsized effects: marker chromosomes are 10 times more common in children with mental retardation than the normal population, and several sSMCs have been associated with known syndromes, such as the inverted duplication 22q associated with cat eye syndrome (see Signature Spotlight below). Unfortunately, due to their small size and varying degrees of mosaicism (most markers are present only in a small number of cells), the characterization of most markers is beyond the reach of FISH and G-banding.
To address this issue, Signature Genomic Laboratories constructed a high-density microarray using 974 bacterial artificial chromosome (BAC) clones targeted to the 43 unique human pericentromeric regions (due to their highly repetitive content, the acrocentric short arms were excluded). Three-clone contigs spaced ~0.5 Mb apart spanned, on average, 5 Mb of the most proximal unique sequence adjacent to the centromere. Signature studied the utility of its new pericentromeric microarray by the characterization of 20 cases with sSMCs that had previously been detected by either conventional chromosome analysis or a targeted microarray.
The study, published in Genetics in Medicine (click here to request a reprint), showed that, in 15 cases, the enhanced coverage of the pericentromeric array could not only identify the provenance of the sSMC but could distinguish between the involvement of the short or long arm of each chromosome. In addition, in several cases, complex rearrangements or multiple markers could be identified. Overall, 18 sSMCs were identified. The expanded coverage of the microarray was sufficient to characterize the breakpoints in two-thirds of sSMCs identified in the study.
The results of the current study suggest that array CGH may more accurately characterize sSMCs than conventional cytogenetic techniques.
Signature Spotlight Case #4: Dicentric marker 22q
This issue's Spotlight Case involves the identification and characterization of a supernumary marker chromosome, demonstrating the clinical application of the Signature MarkerChip™.
The subject is a 9-year 11-month old Hispanic male referred for short stature, repaired imperforate anus, chronic constipation, bilateral undescended testes, unspecified tracheal problems shortly after birth and an ear pit. Prior evaluations showed bone age two standard deviations below chronological age, spinal MRI which was reportedly abnormal, and a rectal biopsy to rule out Hirschsprung’s disease. Karotyping performed at age 7 years showed a small monosatellited dicentric marker chromosome in 100% of cells. FISH performed with probes corresponding to chromosome 15 were negative, clarifying the cytogenetic finding as follows: 47, XY,+mar.ish(15q11.2:SNRPN-, D15Z1-,PML-).
On examination at 9 years 11 months, the child showed height and weight below the third percentile, OFC minus two standard deviations, small face with assymetry, downward-slanting palpebral fissures, right preauricular pit, and clinodactyly of the right fifth finger and left fifth toe. Development was appropriate for his age. Neurological exam was normal.
Microarray analysis using the Signature MarkerChip™ demonstrated a two-copy gain of six BAC clones spanning ~2.2 Mb at 22q11.1q11.21, indicating tetrasomy of proximal 22q (Figure 1). FISH performed with a probe corresponding to the cat-eye syndrome locus on 22q11.1 showed the presence of a marker chromosome 22 in 30/30 (100%) of cells (Figure 2). FISH analysis of interphase nuclei using the same BAC clone showed a signal pattern consistent with tetrasomy 22q. Thus, this subject's marker is a derivative chromosome from two copies of the pericentromeric region of chromosome 22q.
Blake Ballif, Director of Product Development and Research: Experience is Everything
Three years is a long time in the still-young field of microarray diagnostics. When Dr. Blake C. Ballif, Ph.D., came to Signature in 2004, only a handful of research laboratories were using array CGH for the characterization of constitutional chromosomal abnormalities; today, the use of array CGH for research and diagnostics is widespread—a PubMed search for "array CGH" brings back over 700 results from the last three years. Having been in the industry since its inception, Dr. Ballif has seen how far it has come; as Director of Product Development and Research for Signature Genomic Laboratories, he has a hand in shaping in which direction it will go.
"At first, physicians were hesistant to take on array CGH—it was a new, relatively unheard-of technology," Dr. Ballif says. "But in the last couple of years, they've really embraced it. It's been gratifying to see how it's made an impact in diagnostics, especially for those patients who've had all the routine tests done and received a negative result."
The use of microarray technology in the clinical setting has been a learning experience not only for physicians and patients but for members of the industry.
"We have an incredible amount of experience, having done over 10,000 cases. We know how powerful the technology is, and what the limitations of the technology are in a diagnostic setting," Dr. Ballif says. "Despite having had all this experience, we're still surprised at how useful the technology is at identifying chromosomal abnormalities—especially the unexpected things, such as novel microdeletions, reciprocal duplications of known microdeletions, and atypical-sized abnormalities."
The power of microarray technology ensures that such surprises are part of the territory; the key, Dr. Ballif says, is to understand them so that the unpleasant surprises can be avoided before they reach the patient's folder.
"Because it's a new technology, and because the patient is our foremost priority, we've approached the development of our technology cautiously so that we can enhance it as we move forward and still ensure that we provide the best testing for the patient," Dr. Ballif says.
Some of these enhancements will appear on Version 5.0 of Signature's flagship product, the SignatureChip®, which will include increased coverage of a number of clinically relevant genetic loci; Ballif says the new chip should be available later this year.
"It's been very exciting to be involved with Signature because of how rapidly the company has been growing and how rapidly the technology has been accepted by the medical community," Dr. Ballif says.