Limits...
Challenges and solutions for gene identification in the presence of familial locus heterogeneity.

Rehman AU, Santos-Cortez RL, Drummond MC, Shahzad M, Lee K, Morell RJ, Ansar M, Jan A, Wang X, Aziz A, Riazuddin S, Smith JD, Wang GT, Ahmed ZM, Gul K, Shearer AE, Smith RJ, Shendure J, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian GenomicsHinnant J, Khan SN, Fisher RA, Ahmad W, Friderici KH, Riazuddin S, Friedman TB, Wilch ES, Leal SM - Eur. J. Hum. Genet. (2014)

Bottom Line: However, many NGS studies fall short of identifying causal variants, with estimates for success rates as low as 25% for uncovering the pathological variant underlying disease etiology.We demonstrate novel approaches to apply linkage analysis and homozygosity mapping (for autosomal recessive consanguineous pedigrees), which can be used to detect locus heterogeneity using either NGS or SNP array data.Results from linkage analysis and homozygosity mapping can also be used to group sibships or individuals most likely to be segregating the same causal variants and thereby increase the success rate of gene identification.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.

ABSTRACT
Next-generation sequencing (NGS) of exomes and genomes has accelerated the identification of genes involved in Mendelian phenotypes. However, many NGS studies fall short of identifying causal variants, with estimates for success rates as low as 25% for uncovering the pathological variant underlying disease etiology. An important reason for such failures is familial locus heterogeneity, where within a single pedigree causal variants in two or more genes underlie Mendelian trait etiology. As examples of intra- and inter-sibship familial locus heterogeneity, we present 10 consanguineous Pakistani families segregating hearing impairment due to homozygous variants in two different hearing impairment genes and a European-American pedigree in which hearing impairment is caused by four variants in three different genes. We have identified 41 additional pedigrees with syndromic and nonsyndromic hearing impairment for which a single previously reported hearing impairment gene has been identified but only segregates with the phenotype in a subset of affected pedigree members. We estimate that locus heterogeneity occurs in 15.3% (95% confidence interval: 11.9%, 19.9%) of the families in our collection. We demonstrate novel approaches to apply linkage analysis and homozygosity mapping (for autosomal recessive consanguineous pedigrees), which can be used to detect locus heterogeneity using either NGS or SNP array data. Results from linkage analysis and homozygosity mapping can also be used to group sibships or individuals most likely to be segregating the same causal variants and thereby increase the success rate of gene identification.

No MeSH data available.


Related in: MedlinePlus

Two families segregating autosomal recessive hearing impairment where variable phenotype of affected individuals helped to identify intra-familial locus heterogeneity. The box on the lower side shows the legend for genotypes. Genotypes beneath each symbol follow the order and colors of variant names listed above each pedigree. In family 5, a MYO7A frameshift variant segregates with Usher syndrome in branch 1, while the GJB2 c.71G>A (p.(Trp24*)) variant segregates with nonsyndromic hearing impairment in branch 2. Family 6 is from a community isolate, which descended from four ancestors that immigrated to North America from Germany in the seventeenth century. Four NSHI-causal variants segregate in this family. The GJB2 c.35delG haplotype 1 (red) was inherited by 27 of >200 genotyped community members, while GJB2 c.35delG haplotype 2 (black) was identified in 21 genotyped family members who descended from two immigrants originating from nineteenth century Austro-Hungary. Individuals 82 and 96 of family 6 were screened using OtoSCOPE,30 a NGS capture array targeting NSHI and selected hearing impairment syndrome genes, but no causal variants were identified.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC4538203&req=5

fig2: Two families segregating autosomal recessive hearing impairment where variable phenotype of affected individuals helped to identify intra-familial locus heterogeneity. The box on the lower side shows the legend for genotypes. Genotypes beneath each symbol follow the order and colors of variant names listed above each pedigree. In family 5, a MYO7A frameshift variant segregates with Usher syndrome in branch 1, while the GJB2 c.71G>A (p.(Trp24*)) variant segregates with nonsyndromic hearing impairment in branch 2. Family 6 is from a community isolate, which descended from four ancestors that immigrated to North America from Germany in the seventeenth century. Four NSHI-causal variants segregate in this family. The GJB2 c.35delG haplotype 1 (red) was inherited by 27 of >200 genotyped community members, while GJB2 c.35delG haplotype 2 (black) was identified in 21 genotyped family members who descended from two immigrants originating from nineteenth century Austro-Hungary. Individuals 82 and 96 of family 6 were screened using OtoSCOPE,30 a NGS capture array targeting NSHI and selected hearing impairment syndrome genes, but no causal variants were identified.

Mentions: Depending on the phenotype and how many different variants and genes are involved in disease etiology, screening known genes or variants can be a useful tool prior to NGS. For nonsyndromic (NS) HI, causal variants in ~80 genes have been identified and some of these variants are frequent in individuals with NSHI in particular populations, for example, variants in GJB2.2, 3, 15, 16, 17 DNA samples from hearing-impaired family members were initially screened for putatively causal GJB2 variants and, for Pakistani families, common NSHI variants in CIB2, HGF and SLC26A4. Using this approach, we were able to resolve the locus heterogeneity in four families: variants in GJB2 and HGF are responsible for HI in families 1 and 2, while variants in GJB2 and SLC26A4 are responsible for HI in families 3 and 4 (Figure 1). For six additional pedigrees, homozygous or compound heterozygous variants in GJB2 (families 5, 6, 8 and 11), HGF (family 7) or CIB2 (family 9) were initially identified for some but not all hearing-impaired individuals (Figures 2 and 3, Table 2).


Challenges and solutions for gene identification in the presence of familial locus heterogeneity.

Rehman AU, Santos-Cortez RL, Drummond MC, Shahzad M, Lee K, Morell RJ, Ansar M, Jan A, Wang X, Aziz A, Riazuddin S, Smith JD, Wang GT, Ahmed ZM, Gul K, Shearer AE, Smith RJ, Shendure J, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian GenomicsHinnant J, Khan SN, Fisher RA, Ahmad W, Friderici KH, Riazuddin S, Friedman TB, Wilch ES, Leal SM - Eur. J. Hum. Genet. (2014)

Two families segregating autosomal recessive hearing impairment where variable phenotype of affected individuals helped to identify intra-familial locus heterogeneity. The box on the lower side shows the legend for genotypes. Genotypes beneath each symbol follow the order and colors of variant names listed above each pedigree. In family 5, a MYO7A frameshift variant segregates with Usher syndrome in branch 1, while the GJB2 c.71G>A (p.(Trp24*)) variant segregates with nonsyndromic hearing impairment in branch 2. Family 6 is from a community isolate, which descended from four ancestors that immigrated to North America from Germany in the seventeenth century. Four NSHI-causal variants segregate in this family. The GJB2 c.35delG haplotype 1 (red) was inherited by 27 of >200 genotyped community members, while GJB2 c.35delG haplotype 2 (black) was identified in 21 genotyped family members who descended from two immigrants originating from nineteenth century Austro-Hungary. Individuals 82 and 96 of family 6 were screened using OtoSCOPE,30 a NGS capture array targeting NSHI and selected hearing impairment syndrome genes, but no causal variants were identified.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4538203&req=5

fig2: Two families segregating autosomal recessive hearing impairment where variable phenotype of affected individuals helped to identify intra-familial locus heterogeneity. The box on the lower side shows the legend for genotypes. Genotypes beneath each symbol follow the order and colors of variant names listed above each pedigree. In family 5, a MYO7A frameshift variant segregates with Usher syndrome in branch 1, while the GJB2 c.71G>A (p.(Trp24*)) variant segregates with nonsyndromic hearing impairment in branch 2. Family 6 is from a community isolate, which descended from four ancestors that immigrated to North America from Germany in the seventeenth century. Four NSHI-causal variants segregate in this family. The GJB2 c.35delG haplotype 1 (red) was inherited by 27 of >200 genotyped community members, while GJB2 c.35delG haplotype 2 (black) was identified in 21 genotyped family members who descended from two immigrants originating from nineteenth century Austro-Hungary. Individuals 82 and 96 of family 6 were screened using OtoSCOPE,30 a NGS capture array targeting NSHI and selected hearing impairment syndrome genes, but no causal variants were identified.
Mentions: Depending on the phenotype and how many different variants and genes are involved in disease etiology, screening known genes or variants can be a useful tool prior to NGS. For nonsyndromic (NS) HI, causal variants in ~80 genes have been identified and some of these variants are frequent in individuals with NSHI in particular populations, for example, variants in GJB2.2, 3, 15, 16, 17 DNA samples from hearing-impaired family members were initially screened for putatively causal GJB2 variants and, for Pakistani families, common NSHI variants in CIB2, HGF and SLC26A4. Using this approach, we were able to resolve the locus heterogeneity in four families: variants in GJB2 and HGF are responsible for HI in families 1 and 2, while variants in GJB2 and SLC26A4 are responsible for HI in families 3 and 4 (Figure 1). For six additional pedigrees, homozygous or compound heterozygous variants in GJB2 (families 5, 6, 8 and 11), HGF (family 7) or CIB2 (family 9) were initially identified for some but not all hearing-impaired individuals (Figures 2 and 3, Table 2).

Bottom Line: However, many NGS studies fall short of identifying causal variants, with estimates for success rates as low as 25% for uncovering the pathological variant underlying disease etiology.We demonstrate novel approaches to apply linkage analysis and homozygosity mapping (for autosomal recessive consanguineous pedigrees), which can be used to detect locus heterogeneity using either NGS or SNP array data.Results from linkage analysis and homozygosity mapping can also be used to group sibships or individuals most likely to be segregating the same causal variants and thereby increase the success rate of gene identification.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA.

ABSTRACT
Next-generation sequencing (NGS) of exomes and genomes has accelerated the identification of genes involved in Mendelian phenotypes. However, many NGS studies fall short of identifying causal variants, with estimates for success rates as low as 25% for uncovering the pathological variant underlying disease etiology. An important reason for such failures is familial locus heterogeneity, where within a single pedigree causal variants in two or more genes underlie Mendelian trait etiology. As examples of intra- and inter-sibship familial locus heterogeneity, we present 10 consanguineous Pakistani families segregating hearing impairment due to homozygous variants in two different hearing impairment genes and a European-American pedigree in which hearing impairment is caused by four variants in three different genes. We have identified 41 additional pedigrees with syndromic and nonsyndromic hearing impairment for which a single previously reported hearing impairment gene has been identified but only segregates with the phenotype in a subset of affected pedigree members. We estimate that locus heterogeneity occurs in 15.3% (95% confidence interval: 11.9%, 19.9%) of the families in our collection. We demonstrate novel approaches to apply linkage analysis and homozygosity mapping (for autosomal recessive consanguineous pedigrees), which can be used to detect locus heterogeneity using either NGS or SNP array data. Results from linkage analysis and homozygosity mapping can also be used to group sibships or individuals most likely to be segregating the same causal variants and thereby increase the success rate of gene identification.

No MeSH data available.


Related in: MedlinePlus