New reference allelic ladders to improve allelic designation in a multiplex STR system

Griffiths, Richard A.; Barber, M. D.; Johnson, Peter; Gillbard, S. M.; Haywood, Mek; Smith, Christin; Arnold, Johann; Burke, Terry; Urquhart, Andrew J.; Gill, Peter

doi:10.1007/s004140050167

Cited by 62 publications

(25 citation statements)

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“…By far, the best approach is to develop marker-specific size ladders which contain all the common alleles for a given locus. This is the approach used in forensic medicine, and it is not an unrealistic approach for molecular typing, as each system usually involves only a few loci (17,18,25). Ideally, a ladder would be developed for every locus in a given system.…”

Section: Discussionmentioning

confidence: 99%

A Cautionary Tale: Lack of Consistency in Allele Sizes between Two Laboratories for a Published Multilocus Microsatellite Typing System

2007

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For species with low genetic diversity, typing using the differences in PCR fragment length resulting from variations in numbers of short tandem repeats has been shown to provide a high level of discrimination. This technique has been called multilocus microsatellite typing (MLMT) or multiple-locus variable-number tandem repeat analysis, and studies usually employ genetic or sequence analyzers to size PCR fragments to a high degree of precision. We set out to validate one such system that has been developed for Aspergillus fumigatus . The sizes of the alleles were compared both by sequencing and from two genotyping laboratories, where they used capillary electrophoresis (CE) for sizing. Size differences of up to 6 bases were found between the actual sizes reported by sequencing and the sizes reported by CE. In addition, because the two genotyping laboratories used different machines and running conditions, differences of up to 3 bases were identified between them. As the microsatellite markers used differ by repeat units of 3 or 4 bases, it was not possible to assign PCR fragments to the correct alleles without confirming the sizes of a range of alleles by direct sequencing. Lines of best fit were plotted for each CE machine against actual sizes and will therefore enable unsequenced PCR fragments to be assigned to the correct alleles. This study highlights the care required to ensure that an MLMT system undergoes a suitable correction procedure before data can be merged between different laboratories involved in the typing of individual species.

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Section: Discussionmentioning

confidence: 99%

A Cautionary Tale: Lack of Consistency in Allele Sizes between Two Laboratories for a Published Multilocus Microsatellite Typing System

2007

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“…However, the basic repeat structure is different between alleles≤30 and≥30.2. Some alleles are Africanspecific, but their frequencies are low [9,10]. Unlike the FGA locus, groups L and H in the CFI STR are clearly distinguishable by their size and repeat structure.…”

Section: Discussionmentioning

confidence: 99%

A hypervariable STR polymorphism in the complement factor I (CFI) gene: Asian-specific alleles

et al. 2009

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In this study, a short tandem repeat (STR) polymorphism in intron 7 of the human complement factor I (CFI) gene was studied in 637 DNA samples obtained from African, German, Thai, and Japanese populations and German and Japanese families. A total of 41 alleles were observed and classified into two groups, L and H, based on size differences. Group H, which consisted of 16 alleles, was observed only in Thai and Japanese populations at frequencies of 0.162 and 0.116, respectively, and was strongly associated with c.1217A in exon 11 (CFI*Ah). The heterozygosity values ranged from 0.89 in German to 0.93 in Thai populations. This STR would be a useful supplementary marker for forensic individualization.

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“…Each allele in an allelic ladder supplied as part of a commercial kit is usually sequenced by the manufacturer and alleles present in the ladder typically span the expected range of previously observed alleles for that locus (e.g., [2,3]). The alleles present in the allelic ladder are usually sequenced to provide a characterized reference sample [13]. Com- parison to allelic ladders also facilitates recognition of variant types, such as single nucleotide bp insertions or deletions [14].…”

Section: Introductionmentioning

confidence: 99%

Locus‐specific brackets for reliable typing of Y‐chromosome short tandem repeat markers

2005

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Short tandem repeat (STR) loci, widely used as genetic markers in disease diagnostic studies and human identity applications, are traditionally genotyped through comparison of allele sizes to a sequenced allelic ladder. Allelic ladders permit a floating bin allele calling method to be utilized, which enables reliable allele calling across laboratories, instrument platforms, and electrophoretic conditions. Precise sizing methods for STR allele calling involving fixed bins can also be used when a high degree of precision has been demonstrated within an instrument platform and a set of electrophoretic conditions. An alternative method for reliable genotyping of STR markers, locus-specific brackets (LSBs), is introduced here. LSBs are artificial alleles created through molecular biology manipulations to be shorter or longer than alleles commonly seen in populations under investigation. The size and repeat number of measured alleles are interpolated between the two LSB products that are mixed with the polymerase chain reaction-amplified STR alleles. The advantages and limitations of the LSB approach are described along with a concordance study between the LSB typing approach and other STR typing methods. Complete agreement was observed with 162 samples studied at 5 Y-chromosome loci.

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New reference allelic ladders to improve allelic designation in a multiplex STR system

Cited by 62 publications

References 1 publication

A Cautionary Tale: Lack of Consistency in Allele Sizes between Two Laboratories for a Published Multilocus Microsatellite Typing System

A Cautionary Tale: Lack of Consistency in Allele Sizes between Two Laboratories for a Published Multilocus Microsatellite Typing System

A hypervariable STR polymorphism in the complement factor I (CFI) gene: Asian-specific alleles

Locus‐specific brackets for reliable typing of Y‐chromosome short tandem repeat markers

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