Rapid Technology to Identify Structural Chromosome Abnormalities II

Primary pulmonary lymphangiectasia (PPL) is a rare disorder of infancy and childhood caused by an abnormal dilatation of the lymphatics of the lung. The cause of PPL is unknown. A child came to our attention that failed to initiate breathing at birth, was resuscitated, and was subsequently diagnosed with PPL without other anomalies. A karyotype revealed a balanced translocation 46,XY,t(3;14)(q27;q11.2), not present in either parent. The research team developed a novel methodology termed “hybrid SNPing” to resolve the breakpoints, by applying high density single nucleotide polymorphism (SNP) genotyping to human-mouse somatic cell hybrids retaining each translocation chromosome. Hybrid SNPing takes advantage of the differential hybridization and detection of human and mouse DNA to the SNP probes on the chip.

The human SNPs on both recombinant chromosomes are identified to within close proximity to the breakpoint while the rodent DNA typically results in no calls. This technique allowed rapid resolution of the breakpoints to within 2 to 4 kb and full identification of the sequence across both breakpoints with PCR and DNA sequence analysis. Although the t(3;14) translocation did not directly interrupt any gene, the breakpoints localize to conserved non-coding sequences between SALL2 (a putative oncogene) and METTL3 in chromosome 14q11.2 and 5’ of BCL6 (a known oncogene in diffuse large B-cell lymphoma) in 3q27.3.

Balanced translocations within intron 1 of BCL6 and 5’ of the gene have previously been described as causal major and alternative breakpoints, respectively, in B-cell lymphoma. SNP genotype analysis, FISH, and quantitative dosage genomic PCR also identified genome-wide copy number variation (CNV) in this patient with duplication CNV in chromosome 9p24.1 and 16p11.2, and deletion CNV in 1q31.3. These CNV may be incidental or may contribute to the PPL phenotype of this patient. Due to the de novo origin of the translocation, we suggest that genes flanking one or both breakpoints may be deregulated and potentially causal in PPL.

Prinicipal Investigator
Robert Nicholls, PhD

Last Update
August 14, 2010
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Last Update
August 14, 2010