Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing

Abstract

Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma. Whole-genome mate-pair sequencing (WG-MPS) was applied to map the breakpoints in nine two-way ABT carriers from four families. Translocation breakpoints and patient-specific structural variants were validated by Sanger sequencing and quantitative Real Time PCR, respectively. Identical sequencing patterns and breakpoints were identified in affected and non-affected members carrying the same translocations. PTCD1, ATP5J2-PTCD1, CADPS2, and STPG1 were disrupted by the translocations in three families, rendering them initially as possible disease candidate genes. However, subsequent mutation screening and structural variant analysis did not reveal any pathogenic mutations or unique variants in the affected individuals that could explain the phenotypic differences between carriers of the same translocations. In conclusion, we suggest that NGS-based methods, such as WG-MPS, can be successfully used for detailed mapping of translocation breakpoints, which can also be used in routine clinical investigation of ABT cases. Unlike de novo translocations, no associations were determined here between familial two-way ABTs and the phenotype of the affected members, in which the presence of cryptic imbalances and complex chromosomal rearrangements has been excluded. Future whole-exome or whole-genome sequencing will potentially reveal unidentified mutations in the patients underlying the discordant phenotypes within each family. In addition, larger studies are needed to determine the exact percentage for phenotypic risk in families with ABTs.

A Genome Model Linking Birth Defects to Infections

“…Data Sources. DNA sequences from acquired congenital disorders were from published whole genome sequences at chromosome breakpoints and rearrangement sites [1][2][3] . Comparison to multiple databases of microbial sequences determined whether there was significant human homology.…”

“…Emphasis was on cases with strong evidence that a particular human chromosome rearrangement was pathologic for the congenital disorder. Patients in the 3 major studies [1][2][3] used in this analysis were 98 females and 144 males.…”

“…Genome sequencing of the entire family may be necessary 3 The graph at the right shows the quantitive differences created by the rearrangement. Microorganisms are arranged alphabetically.…”

“…As the nervous system develops, tion of the neurologic system. Based on DNA sequence analyses, some chromosome rearrangements have been identified as causing individual congenital disorders because they disrupt genes essential for normal development [1][2][3] . There is poor understanding and no effective treatment for many of these overwhelming abnormalities.…”

Parental infections disrupt clustered genes encoding related functions required for nervous system development in newborns

“…A significant advance in genome sequence level resolution of balanced cytogenetic abnormalities greatly improves the ability to document changes in regulation and dosage for genes critical to the function of the neurologic system. Based on DNA sequence analyses, some chromosome rearrangements have been identified as causing individual congenital disorders because they disrupt genes essential for normal development [1][2][3] .…”