Development of a multiplex panel with 36 insertion/deletion markers (InDel) for individual identification

Filoğlu, Gönül; Duvenci, Arzu; Tas, Sebahat; Karadayi, H.; Aşıcıoğlu, Faruk; Bülbül, Özlem

doi:10.1007/s12024-023-00652-z

Cited by 2 publications

(1 citation statement)

References 30 publications

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“…Hematin was table to obtain full recovery up to 21 μM of input at 57 μM there was a drop in recovery to 73%. In comparison to other INDEL panels, the developed panel is not resistant to hematin or humic acid to the same degree [44,45]. Studies using 24plex have at 1 ng, shown higher recovery than the INDEL panel for the same inhibitors [46,47].…”

Section: Challenging Samplesmentioning

confidence: 87%

Development of a novel five‐dye panel for human identification insertion/deletion (INDEL) polymorphisms

Avellaneda,

Johnson,

Gutierrez

et al. 2024

Journal of Forensic Sciences

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DNA analysis of forensic case samples relies on short tandem repeats (STRs), a key component of the combined DNA index system (CODIS) used to identify individuals. However, limitations arise when dealing with challenging samples, prompting the exploration of alternative markers such as single nucleotide polymorphisms (SNPs) and insertion/deletion (INDELs) polymorphisms. Unlike SNPs, INDELs can be differentiated easily by size, making them compatible with electrophoresis methods. It is possible to design small INDEL amplicons (<200 bp) to enhance recovery from degraded samples. To this end, a set of INDEL Human Identification Markers (HID) was curated from the 1000 Genomes Project, employing criteria including a fixation index (FST) ≤ 0.06, minor allele frequency (MAF) >0.2, and high allele frequency divergence. A panel of 33 INDEL‐HIDs was optimized and validated following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, utilizing a five‐dye multiplex electrophoresis system. A small sample set (n = 79 unrelated individuals) was genotyped to assess the assay's performance. The validation studies exhibited reproducibility, inhibition tolerance, ability to detect a two‐person mixture from a 4:1 to 1:6 ratio, robustness with challenging samples, and sensitivity down to 125 pg of DNA. In summary, the 33‐loci INDEL‐HID panel exhibited robust recovery with low‐template and degraded samples and proved effective for individualization within a small sample set.

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Section: Challenging Samplesmentioning

confidence: 87%

Development of a novel five‐dye panel for human identification insertion/deletion (INDEL) polymorphisms

Avellaneda,

Johnson,

Gutierrez

et al. 2024

Journal of Forensic Sciences

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InDEL instability in two different tumoral tissues and its forensic significance

Gürel,

Aşıcıoğlu,

Ersoy

et al. 2024

Forensic Sci Med Pathol

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There may be cases where malignant tumor samples can be used for forensic DNA profiling studies. STRs are the first systems preferred in forensic science laboratories for identification purposes. However, genetic instability in tumoral tissues causes STR polymorphism to change, leading to erroneous results. On the other hand, insertion/deletion polymorphism (InDels) are used as genetic markers in forensic science, as they have features that make both STR and SNPs preferable. Although previous studies approved that STR instability is observed in many different tumors, there are only a few studies that have displayed the instability of InDels in tumoral tissues before. In this study, it was aimed to determine whether instability is observed in formalin-fixed paraffin-embedded breast and thyroid tumoral tissues at 36plex InDel Panel. A total of 47 cases, 26 of which were diagnosed as breast cancer and 21 as thyroid cancer, were included in the study. In 21 of 26 (80.76%) breast cancers mutational changes were observed, however only 6 of 21 (28.57%) thyroid carcinoma cases displayed instability.Moreover, in these six cases, mutations were detected at only 1 or 2 loci. The most common change in both tissues was loss of heterozygosity. These findings suggest that paraffin embedded tissues of thyroid tumor can be used in cases of forensic genetic identification, however paraffin embedded breast cancer tissues should be examined with care. In conclusion, low InDel mutation rates compared to STR instability, make InDel analysis from paraffin blocks suitable for forensic genetic identification. However, researchers should keep in mind that there may be differences between the profiles of the tumoral tissues taken as reference and the actual case. In addition, by incorporating additional markers such as SNPs and microhaplotypes with low mutation rates into the study alongside Indels, researchers can significantly enhance the discrimination power in identification processes.

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Development of a multiplex panel with 36 insertion/deletion markers (InDel) for individual identification

Cited by 2 publications

References 30 publications

Development of a novel five‐dye panel for human identification insertion/deletion (INDEL) polymorphisms

Development of a novel five‐dye panel for human identification insertion/deletion (INDEL) polymorphisms

InDEL instability in two different tumoral tissues and its forensic significance

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