Human Short Tandem Repeat (STR) Markers for Paternity Testing in Pig-Tailed Macaques

Candida krusei is a human pathogenic yeast that can cause candidemia with the lowest 90-day survival rate in comparison to other Candida species. Infections occur frequently in immunocompromised patients and several C. krusei outbreaks in health care facilities have been described. Here, we developed a short tandem repeat (STR) typing scheme for C. krusei to allow for fast and cost-effective genotyping of an outbreak and compared identified relatedness of ten isolates to SNP calling from whole-genome sequencing (WGS). From a selection of 14 novel STR markers, six were used to develop two multiplex PCRs. Additionally, three previously reported markers were selected for a third multiplex PCR. In total, 119 C. krusei isolates were typed using these nine markers and 79 different genotypes were found. STR typing correlated well with WGS SNP typing, as isolates with the same STR genotype varied by 8 and 19 SNPs, while isolates that differed in all STR markers varied at least tens of thousands of SNPs. The STR typing assay was found to be specific for C. krusei , stable in 100 subcloned generations, and comparable to SNP calling by WGS. In summary, this newly developed C. krusei STR typing scheme is a fast, reliable, easy-to-interpret and cost-effective method compared to other typing methods. Moreover, the two newly developed multiplexes showed the same discriminatory power as all nine markers combined, indicating that multiplexes M3-1 and M9 are sufficient to type C. krusei .

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Paternity testing usingmassively parallel sequencingand the PowerSeq™ AUTO/Y system for short tandem repeat sequencing

Electrophoresis ◽

10.1002/elps.201800072 ◽

2018 ◽

Vol 39 (21) ◽

pp. 2669-2673 ◽

Cited By ~ 4

Author(s):

Deborah S. B. S. Silva ◽

Fernanda R. Sawitzki ◽

Melissa K. R. Scheible ◽

Sarah F. Bailey ◽

Clarice S. Alho ◽

...

Keyword(s):

Tandem Repeat ◽

Short Tandem Repeat ◽

Paternity Testing ◽

Short Tandem

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Chimerism Monitoring by Short Tandem Repeat (STR) Markers in Allogeneic Stem Cell Transplantation

Clinical Laboratory ◽

10.7754/clin.lab.2018.180409 ◽

2018 ◽

Vol 64 (09/2018) ◽

Author(s):

Raluca Dumache ◽

Alexandra Enache ◽

Ligia Barbarii ◽

Carmen Constantinescu ◽

Andreea Pascalau ◽

...

Keyword(s):

Stem Cell ◽

Stem Cell Transplantation ◽

Cell Transplantation ◽

Allogeneic Stem Cell Transplantation ◽

Tandem Repeat ◽

Short Tandem Repeat ◽

Str Markers ◽

Short Tandem

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Mitochondrial DNA Minisatellites Showed Higher Informativeness and Sensitivity Than the Nuclear DNA Markers for the Quantitative Determination of Chimerism After Allogeneic Stem Cell Transplantation,

Blood ◽

10.1182/blood.v118.21.4004.4004 ◽

2011 ◽

Vol 118 (21) ◽

pp. 4004-4004

Author(s):

Hye Ran Kim ◽

Eun-Jeong Won ◽

Hyun-Jung Choi ◽

Hwan-Young Kim ◽

James Moon ◽

...

Keyword(s):

Mitochondrial Dna ◽

Stem Cell ◽

Stem Cell Transplantation ◽

Quantitative Determination ◽

Allogeneic Stem Cell Transplantation ◽

Tandem Repeat ◽

Short Tandem Repeat ◽

Str Markers ◽

Short Tandem

Abstract Abstract 4004 Background: Mitochondrial DNA (mtDNA) is widely used in forensic identification and anthropologic studies on account of its abundance resulting in preferential amplification, sequencing and inherent variability. We developed mtDNA markers to monitor donor cell engraftment after allogeneic stem cell transplantation(SCT), then compared with nuclear short tandem repeat (STR) markers. Patients and methods: The mtDNA control regions and six mtDNA minisatellites (mtMS) (303 poly C, 16184 poly C, 514 (CA) repeat, 3566 poly C, 12385 poly C and 12418 poly A) from the total DNA samples of 215 cases (donor, recipient and after allogeneic SCT) were amplified using the designated specific primers and PCR. The results were compared with those from the six short tandem repeat (STR) markers (D12S391, D18S51, F13A1, HUM RENA-4, HUM FABP2 and Amelogenin). Results: Polymorphisms in the mtDNA control region identify an informative marker in 88% (189 cases) of all cases. Among the six mtMS markers, the informativeness of 303 poly C and 16184 poly C mtMS was 63% and 67% respectively. A combination of direct sequencing through the mtDNA control region, 303poly C and 16184 poly C mtMS could completely distinguish the donor cells from the recipient cells. The results from a typical mixing experiment to determine the sensitivity revealed a detection limit (DL) of the gene scan analysis in a mtDNA mixture to be visible at 1% heteroplasmy in 303 poly C mtMS marker. However, the DL from D12S391 in the same mixing experiment was 5–10% heteroplasmy. Conclusions: mtMS markers, especially 303 poly C and 16184 poly C markers, can provide a sensitive, accurate and quantitative determination of mixed chimerism after a SCT. Disclosures: No relevant conflicts of interest to declare.

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