A new set of markers for human identification based on 32 polymorphic Alu insertions

Mamedov, Ilgar Z.; Shagina, Irina; Kurnikova, Marya A; Novozhilov, Sergey; Shagin, Dmitry A.; Lebedev, Yuri B.

doi:10.1038/ejhg.2010.22

Cited by 22 publications

(21 citation statements)

References 33 publications

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“…Reliable methods for genetic identification are necessary, in addition to STR genotyping using commercial kits, given the large amount of genetic variation in populations. Strategies with high discriminatory power use additional STRs or biallelic markers, such as SNPs, indels, and Alu insertions .…”

Section: Discussionmentioning

confidence: 99%

Universal fluorescent labeling of amplification products using locked nucleic acids

et al. 2013

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Amplification/hybridization-based genetic analyses using primers containing locked nucleic acids (LNAs) present many benefits. Here, we developed a novel design for universal fluorescent PCR using LNAs. Universal fluorescent PCR generates intermediate nonlabeled fragments and final fluorescent fragments in a two-step amplification process that uses locus-specific primers with universal tails and universal fluorescent primers. In this study, a few standard nucleotides were replaced with LNAs only in the fluorescent universal primers. The sequence of the fluorescent universal primer significantly affected the amplification efficiency. For primers with three LNAs, the fluorescent primers with stable M13(-47) sequences provided the most efficient signal (approximately tenfold higher than the primers with M13(-21) sequences at lower Tm values). Moreover, AT-rich LNA substitutions in the fluorescent primers produced much lower amplification efficiencies than GC-rich substitutions. GC-rich LNAs produced greater differences in Tm values among primers, and resulted in the preferential production of fluorescently labeled amplicons. The specificity and sensitivity of LNA-containing fluorescent primers were assessed by genotyping eight STRs in Japanese individuals, and full STR profiles could be generated using as little as 0.25 ng of genomic DNA. The method permitted clear discrimination of alleles and represents sensitive STR genotyping at a reduced cost.

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Section: Discussionmentioning

confidence: 99%

Universal fluorescent labeling of amplification products using locked nucleic acids

et al. 2013

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“…Initial efforts towards marker selection focused on the set of forensic candidate markers described by Mamedov et al [16] . Using these markers as a benchmark and the previously described Mini-Primer strategy, an attempt was made to reduce the amplicon size of a subset of markers reported by Mamedov et al [16] .…”

Section: Marker Selection and Pcr Optimizationmentioning

confidence: 99%

“…Using these markers as a benchmark and the previously described Mini-Primer strategy, an attempt was made to reduce the amplicon size of a subset of markers reported by Mamedov et al [16] . Primers for 5 markers were designed such that all amplicons were less than 120 bp in size for both the insertion and null alleles (online suppl.…”

Section: Marker Selection and Pcr Optimizationmentioning

confidence: 99%

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INNULs: A Novel Design Amplification Strategy for Retrotransposable Elements for Studying Population Variation

et al. 2012

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Objectives: Retrotransposable elements (REs), consisting of long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), are a group of markers that can be useful for human identity testing. Until now, however, due to the inherent size difference (up to 6 kb in some instances) associated with insertion and null alleles (or INNULs), the use of REs for facilitated population studies has not been sought or practical. The size of the insertion elements (from a few hundred to several thousand bp) has proven to limit their utility as a marker because of the inefficient amplicon yield with PCR. A novel primer design now facilitates INNUL marker testing. A preliminary panel of single-locus markers was developed to evaluate the potential of typing these insertion elements. Nine INNULs (5 Alu and 4 LINEs) were typed in three major North American populations and analyzed for population genetic features. In addition, the variation of each marker among the sample populations provides insight of its potential use as individual identification or ancestral marker. Methods: INNUL markers were developed into fluorescently labeled single-loci PCR. Nine markers were developed with amplicons that were less than 180 bp in length, and, depending on the locus amplicons of the INNULs, alleles varied in size from 50 to 1 bp. This allele size is noteworthy because the insertion alleles of the 9 loci range in size from 297 to 6,195 bp. The allele distribution of the INNULs was assessed and analyzed in three major North American populations. Results: Upon observation of the distribution of the alleles in three major North American populations, the markers generally met Hardy-Weinberg expectations, and there was little evidence of detectable levels of linkage disequilibrium. Due to varying distributions of the alleles in the major population groups tested, some of the markers might be better suited for use as an individual identification marker, while others are better suited for bio-ancestral studies. Conclusions: Using the primer design strategy described in our work, SINEs and (for the first time, to our knowledge) LINEs can be utilized as markers for studying population genetic variation that is more amenable to the limitations of the PCR technique. This study lays the foundation for future work of developing a multiplex panel of INNUL markers that can be used as a single-tube assay for human identity testing utilizing small amplicons (<180 bp), which could be useful for ancient or degraded forensic DNA samples.

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“…Such markers are broadly used in pop ulation studies, parental testing and genetic certifica tion [20,21]. The search for associations with various phenotypes, including mono and polygenic diseases, and functional analysis of MMs adds to their potential in predisposition detection, early detection of dis eases, choice of treatment options, etc.…”

Section: Design Of Molecular Markersmentioning

confidence: 99%

Functional analysis of polymorphic insertions of Alu retroelements in acute lymphoblastic leukemia patients

et al. 2012

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Human genome variability observed within patient cohorts is considered as a goal of functional genomics essential for personalized medicine progress. In the current research we implement functional analysis of 31 polymorphic Alu insertions located within gene introns for individual genomes of patients with acute lymphoblastic leukemia (ALL). As a result we demonstrated a decrease of the primary transcripts content for 21 Alu-containing alleles. The most strong inhibitory effect of 10 Alu insertions was observed in both mononuclear blood cells of healthy donors and B-lymphoblasts of ALL patients. Allele frequencies of three Alu insertions that are located in MEF2C (two of them) and TAX1BP1 genes significantly differ (p-value 0.027. 0.052. 0.014 accordingly) between cohorts of healthy donors and ALL patients. Prolong influence of the Alu insertions on intracellular content of mature mRNA was studied for corresponding allele of TARBP1 gene.

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A new set of markers for human identification based on 32 polymorphic Alu insertions

Cited by 22 publications

References 33 publications

Universal fluorescent labeling of amplification products using locked nucleic acids

Universal fluorescent labeling of amplification products using locked nucleic acids

INNULs: A Novel Design Amplification Strategy for Retrotransposable Elements for Studying Population Variation

Functional analysis of polymorphic insertions of Alu retroelements in acute lymphoblastic leukemia patients

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