Characterization of Apparently Balanced Chromosomal Rearrangements from the Developmental Genome Anatomy Project

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.

Human Structural Variation: Mechanisms of Chromosome Rearrangements

“…Three unbalanced translocations had breakpoints consistent with NAHR between pairs of LINEs, HERVs, or short SDs; however, most breakpoint junctions had blunt ends, microhomology, inserted sequence, or inversions, indicating that most unbalanced translocations arise by NHEJ or MMBIR. These breakpoint signatures are similar to those from sequenced balanced translocations [51–53]. On the other hand, sequencing another cohort of nine unbalanced translocations revealed that six were mediated by NAHR between 6 kb LINE, 3 kb HERV, or 1.7 kb SD pairs that are each >90% identical [45].…”

“…In both unbalanced translocation studies, LINE and HERV elements were capable of NAHR, whereas no Alu – Alu events were detected [45,46]. Indeed, Alu – Alu recombination has been reported in only three translocations [53–55]. This trend suggests that, for NAHR-mediated rearrangements, those that are interchromosomal may require longer stretches of homology and greater sequence identity than those that are intrachromosomal.…”

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

“…All large-insert sequencing methods allowed generation of paired-end reads with median insert size of 2.5–3.5 kb as opposed to 300 bp using conventional methods. A subset of samples were prepared with standard short-insert paired-end protocols (n=12) or targeted sequencing of the breakpoints based on previous positional cloning to narrow the breakpoint regions (n=34), as previously described 7,11,81 . Of note, 87 BCAs had been initially reported in the literature, though many had not been mapped to sequence resolution (Supplementary Table 1).…”

Reciprocal Translocation Carrier Diagnosis in Preimplantation Human Embryos

“…Several techniques had been developed to map chromosome breakpoints to the kilobase level (Chen et al, 2008, Gribble et al, 2009, Higgins et al, 2008, Sobreira et al, 2011, Talkowski et al, 2011, Talkowski et al, 2012, Vergult et al, 2014). However, these techniques are time-consuming, expensive, and do not provide information about the breakpoint-linked SNPs for use in later PGDs.…”