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(A) Scaled representation of <t>GBA1,</t> MTX1 , and their highly homologous pseudogenes. MTXP lies in the 16 kb region between GBA1 and GBAP1 . MTX1 and MTXP are transcribed in the direction opposite to that of GBA1 and GBAP1 . (B) Example of a reciprocal crossover event, resulting in a (i) gene-pseudogene fusion allele and a (ii) duplicated allele. These recombinant alleles are difficult to detect using next-generation sequencing methods. Sequence reads containing the pseudogene-derived segment (red) of the recombinant alleles may align to the pseudogene instead. This can lead to false negatives and reduce the read depth of GBA1 . In this example, reads containing the 55 bp deletion from the recombinant alleles may align preferentially to the pseudogene (Adapted in part from Tayebi et al., ).
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(A) Scaled representation of GBA1, MTX1 , and their highly homologous pseudogenes. MTXP lies in the 16 kb region between GBA1 and GBAP1 . MTX1 and MTXP are transcribed in the direction opposite to that of GBA1 and GBAP1 . (B) Example of a reciprocal crossover event, resulting in a (i) gene-pseudogene fusion allele and a (ii) duplicated allele. These recombinant alleles are difficult to detect using next-generation sequencing methods. Sequence reads containing the pseudogene-derived segment (red) of the recombinant alleles may align to the pseudogene instead. This can lead to false negatives and reduce the read depth of GBA1 . In this example, reads containing the 55 bp deletion from the recombinant alleles may align preferentially to the pseudogene (Adapted in part from Tayebi et al., ).

Journal: Frontiers in Genetics

Article Title: Next-Generation Sequencing Analysis of GBA1 : The Challenge of Detecting Complex Recombinant Alleles

doi: 10.3389/fgene.2021.684067

Figure Lengend Snippet: (A) Scaled representation of GBA1, MTX1 , and their highly homologous pseudogenes. MTXP lies in the 16 kb region between GBA1 and GBAP1 . MTX1 and MTXP are transcribed in the direction opposite to that of GBA1 and GBAP1 . (B) Example of a reciprocal crossover event, resulting in a (i) gene-pseudogene fusion allele and a (ii) duplicated allele. These recombinant alleles are difficult to detect using next-generation sequencing methods. Sequence reads containing the pseudogene-derived segment (red) of the recombinant alleles may align to the pseudogene instead. This can lead to false negatives and reduce the read depth of GBA1 . In this example, reads containing the 55 bp deletion from the recombinant alleles may align preferentially to the pseudogene (Adapted in part from Tayebi et al., ).

Article Snippet: GBA1 is located in a gene-rich region on chromosome 1q21 that encompasses seven genes and two pseudogenes within an 85-kb region (Winfield et al., ).

Techniques: Recombinant, Next-Generation Sequencing, Sequencing, Derivative Assay