Indels

A multiplex panel of short-amplicon insertion-deletion DNA polymorphisms for forensic analysis

V. R. D. Santos, Pena, H. B., and Pena, S. D. J., A multiplex panel of short-amplicon insertion-deletion DNA polymorphisms for forensic analysis, vol. 14, pp. 2947-2952, 2015.

We have previously developed a panel of 40 insertion-deletion (INDEL) human DNA polymorphisms that was proven to ad­equately cover the span of global human genetic diversity. The panel was found to have very low matching probabilities with respect to both the global and Brazilian populations. To optimize the panel for application with degraded DNA samples, which are commonly encountered in fo­rensic analysis, we have significantly reduced the amplicon size of the INDELs and developed a new multiplex panel.

Genome-wide polymorphisms between the parents of an elite hybrid rice and the development of a novel set of PCR-based InDel markers

K. Wang, Zhuang, J. Y., Huang, D. R., Ying, J. Z., and Fan, Y. Y., Genome-wide polymorphisms between the parents of an elite hybrid rice and the development of a novel set of PCR-based InDel markers, vol. 14, pp. 3209-3222, 2015.

Genome-wide re-sequencing of the Zhenshan 97 (ZS97) and Milyang 46 (MY46) parents of an elite three-line hybrid rice developed in China resulted in the generation of 9.91 G bases of data with an effective sequencing depth of 11.66x and 11.51x, respectively. Detection of genome-wide DNA polymorphisms, single nucleotide polymorphisms (SNPs), short insertions/deletions (InDels; 1-5 bp), and structural variations (SVs), which is an invaluable variation resource for genetic research and molecular marker-assisted breeding, was conducted by comparing whole-genome re-sequencing data.

Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms

J. R. Pimenta and Pena, S. D. J., Efficient human paternity testing with a panel of 40 short insertion-deletion polymorphisms, vol. 9, pp. 601-607, 2010.

We developed a panel of 40 multiplexed short insertion-deletion (indel) polymorphic loci with widespread chromosomal locations and allele frequencies close to 0.50 in the European population. We genotyped these markers in 360 unrelated self-classified White Brazilians and 50 mother-child-probable father trios with proven paternity. The average heterozygosity (gene diversity) per locus was 0.48, and the combined probability of identity (matching probability) for the 40-locus set was 3.48 x 10-17. The combined power of exclusion of the indel panel was 0.9997.

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