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Feature Articles : Jan 15, 2013 (Vol. 33, No. 2)

Resequencing Still Being Targeted

  • Vicki Glaser

Targeted resequencing is a method of zooming in on regions of interest in a genomic library and sequencing target samples to identify common and rare variants that may be linked to disease.

Several poster presentations at the recent “American Society of Human Genetics” (ASHG) meeting featured this approach as a follow-up to genome-wide association studies (GWAS), to complement whole exome sequencing, to improve the molecular diagnostics of congenital and inherited disorders, and to identify candidate genes and mutations associated with a range of diseases.

A team of researchers from Children’s Hospital of Philadelphia (CHOP) and CHOP Research Institute used fluorescence automated sequencing to sequence the exons of tumor necrosis factor receptor superfamily (TNRFSF)6B in samples from children with inflammatory bowel disease (IBD) and from healthy controls. TNFRSF6B codes for a secreted protein (decoy receptor 3, DcR3) that can neutralize inflammation-inducing cytokines also produced by the TNF superfamily. A common variant in the TNFRSF6B locus, identified with GWAS, has been linked to IBD, and particularly to one form of IBD—pediatric-onset Crohn’s disease.

The group from CHOP used targeted resequencing of TNFRSF6B to identify rare missense mutations that have functional significance—mutations that disrupt the secretion of DcR3 or the ability of the decoy receptors to bind to their target proinflammatory cytokines: TL1A, LIGHT, and Fas ligand.

Christopher Cardinale, M.D., Ph.D., and colleagues opted for a “brute force, old-fashioned Sanger sequencing” approach to search for uncommon, functionally relevant variants to ensure that they would not overlook a single nucleotide substitution that might be missed with genotyping studies, he explained. Once variants were identified, the authors tested them in functional assays that could “point to the role of the locus in the biology of the disease,” Dr. Cardinale said.

They identified 11 missense variants in the TNFRSF6B locus among samples from 532 children with Crohn’s disease. Comparisons of the variants to the wild-type locus in cell culture studies showed that five of the variants were secretion-defective. This suggests that when these mutations are present, the decoy receptors are not secreted and cannot block the proinflammatory effects of their cytokine ligands, contributing to the pathology associated with Crohn’s disease. In this study, the load of missense variations was three times greater among the Crohn’s cases compared to the controls (1.8% vs. 0.54%).

Glycosylation Disorders

Congenital disorders of glycosylation (CDG) represents a group of more than 30 autosomal recessive disorders caused by a deficiency in glycosylation. About one in five affected patients will die before reaching the age of five years due to organ dysfunction. Emory Genetics Laboratory began testing for 25 CDG genes in 2010 using single gene testing and next-generation sequencing (NGS) methods. Melanie Jones, Ph.D., and colleagues from Emory University School of Medicine and Sanford-Burnham Medical Research Institute, presented their findings.

Based on analysis of 118 patient samples, the clinical laboratory identified disease-causing mutations in several of the CDG genes. Sixty-two patients were referred for single-gene sequencing: 11 of those patients had two mutations in a known CDG gene, and 51 patients were negative for two mutations on screening. Fifty-six patients were referred for NGS panel testing: three patients had two mutations in a known CDG gene, 24 patients had one or more variants of unknown clinical significance, and 29 patients had negative test results.

In the research setting, a combination of biochemical and whole exome sequencing is being used to study 39 patients in whom no mutation was found in any of the known CDG genes. The whole exome sequencing approach focused on a library of 250 glycosylation-associated genes and led to the identification of mutations in two genes that were not previously associated with CDG.

One patient had mutations in the DDOST gene, and five patients had mutations in the PIGL gene and had CHIME syndrome, which has clinical features similar to one form of CDG. Among the 39 patients in whom whole exome sequencing was performed, mutations were found in known CDG genes in six patients. Exome analysis is continuing on the remaining patients.

The combination of single gene sequencing and NGS in the clinical setting led to identification of the disease-causing gene defect in 12.7% of patients, whereas whole exome sequencing in the research laboratory identified the gene defect in 30% of patients tested. Unlike NGS panel testing, however, in which all exons are covered, whole exome sequencing can miss some exons, and a mutation in a disease-causing gene could be missed. The group at Emory Genetics Lab recently created an enhanced clinical exome that covers all exons of genes associated with disease.

The number of CDG genes included in diagnostic testing is now at 38, according to Dr. Jones.

Genome-wide association studies of populations affected by schizophrenia have led to the identification of a region of genetic variability on chromosome 6p22 spanning 27–32 Mbp. Most of the GWAS signals detected in this region are likely due to common variants in the population, but targeted resequencing may reveal rare mutations of functional significance. Common variants may often be protective and present at higher frequencies in nonaffected than in affected individuals.

A group of researchers from Virginia Commonwealth University School of Medicine, Health Research Board in Ireland, and Queens University in the U.K. focused on the NF-kappaB (NFκB) activating protein-like (NKAPL) gene, which was identified as a locus of schizophrenia-related common variants in a GWAS of a Han Chinese population.

They amplified and sequenced a 10 kb amplicon containing NKAPL in a sample of Irish schizophrenia cases (538) and Irish controls (567), validated specific variants, and detected novel functional variants in a schizophrenia GWAS locus. Sequencing was performed on a 316 chip to about 100x coverage using the Ion Torrent (Life Technologies) PGM instrument. The researchers reported a pattern of associated rare variation across the entire 10 kb amplicon and in the NKAPL gene. Most of the variants were present at a rate of 0.3–1%, and much of the variation driving the association was more prevalent in control samples.

One functional SNP identified in NKAPL from the Han Chinese GWAS data was found to be rarer in the Irish population, with a 4.2% allele frequency in Irish schizophrenia case samples and no alleles in control samples. Overall, the Irish cases had a greater burden of rare variants (59 alleles)—defined as present in <2% of samples—compared to controls (24 alleles). Based on this finding, the researchers concluded that rare variants across the NKAPL locus might contribute to the higher occurrence of schizophrenia risk.

A team of scientists at Fluidigm discussed the use of an integrated fluidic circuit (IFC) platform for simultaneous amplification of 48 DNA samples using 48 primer sets per run to generate libraries for next-generation sequencing. The group described single-step NGS library preparation in which each reaction includes a target-specific primer pair and a sample-specific barcode primer pair and generates 2,304 unique amplicons in four hours. The two-step multiplex amplification of six sets of 480 assays in parallel yields up to 23,040 unique amplicons.

The six targeted resequencing libraries generated were then tested on five NGS instruments in a total of 16 sequencing reactions and showed uniform performance across platforms. Both amplicon length and GC content affect the number of reads per amplicon, with amplicon length having a more dramatic effect. Overall, the library preparation yielded uniform amplification coverage of target-specific regions.

The PCR reactions take place in 35 nL volume chambers on the IFC. Loading the samples and Master Mix into the contained chambers minimizes the risk of cross-contamination between samples, according to Camila Friedlander, Ph.D., a scientist at Fluidigm.