Rapid screening for Native American mitochondrial and Y-chromosome haplogroups detection in routine DNA analysis

Zuccarelli, Gala; Alechine, Evguenia; Caputo, Mariela; Bobillo, Cecilia; Corach, Daniel; Sala, Andrea

doi:10.1016/j.fsigen.2010.08.018

Cited by 28 publications

(22 citation statements)

References 12 publications

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“…All of these mutations appear only once in PhyloTree Build 13 and have Soares et al [11] scores of at most 2, so that recurrent mutations at these sites are not likely to blur a multiplex analysis. In particular, a reliable recognition of Native American mtDNA haplogroups in multi-ethnic populations cannot make do with just five mtDNA coding-region sites [30]. Finding perfect matches in fragments http://www.google.com/ Enter truncated profile (e.g., "'73G 263G 315.1C 489C 573.1C 573.2C'" or "'A73G A263G 315.1C T489C 573.1C 573.2C'") Finding related partial profiles http://www.google.com/ Enter partial profile (e.g., "A73G G94A PhyloTree" or "A73G G94A mtDNA" or "73G 94A mtDNA") Finding specific variant http://www.google.com/ Search variant (e.g.…”

Section: Multiplex Genotyping Designmentioning

confidence: 99%

Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics

2012

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Haplogrouping refers to the classification of (partial) mitochondrial DNA (mtDNA) sequences into haplogroups using the current knowledge of the worldwide mtDNA phylogeny. Haplogroup assignment of mtDNA control-region sequences assists in the focused comparison with closely related complete mtDNA sequences and thus serves two main goals in forensic genetics: first is the a posteriori quality analysis of sequencing results and second is the prediction of relevant coding-region sites for confirmation or further refinement of haplogroup status. The latter may be important in forensic casework where discrimination power needs to be as high as possible. However, most articles published in forensic genetics perform haplogrouping only in a rudimentary or incorrect way. The present study features PhyloTree as the key tool for assigning control-region sequences to haplogroups and elaborates on additional Web-based searches for finding near-matches with complete mtDNA genomes in the databases. In contrast, none of the automated haplogrouping tools available can yet compete with manual haplogrouping using PhyloTree plus additional Web-based searches, especially when confronted with artificial recombinants still present in forensic mtDNA datasets. We review and classify the various attempts at haplogrouping by using a multiplex approach or relying on automated haplogrouping. Furthermore, we re-examine a few articles in forensic journals providing mtDNA population data where appropriate haplogrouping following PhyloTree immediately highlights several kinds of sequence errors.

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Section: Multiplex Genotyping Designmentioning

confidence: 99%

Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics

2012

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“…From the acquired data, a melting curve was plotted for each sample by calculating the derivative dF/dT for each data point using the RotorGene 6000 software. The results, depicted in Figure (Zuccarelli, Alechine et al 2011) 3.5.5. BLOOD CULTURE 1mL of blood sample with heparin was cultured in a flask with 10mL Iscoves Medium, 100µL PHA and 2 drops of heparin for 71.5h in a 37°C oven and CO2 atmosphere.…”

Section: Y-chromosome Haplogroup Screening (Q R and I)mentioning

confidence: 96%

“…Among others, a novel approach to perform a rapid screening of specific haplogroup-characterizing SNPs has been described. By means of Real Time PCR amplification and subsequent High Resolution Melting (HRM) analysis, it is possible to assign a peak to each SNP allele and therefore identify the haplogroup of each sample (Zuccarelli, Alechine et al 2011). …”

Section: Y Chromosome Haplogroupsmentioning

confidence: 99%

“…It is still unknown whether America was settled from a single founder lineage or if the haplogroup Q1a3a1 had higher fitness than other migrating lineages and was the only paternal lineage that survived through thousands of years in this continent. (Corach et al 2010) With newly developed genetic tools, by Real Time PCR, it is possible to screen the urban population looking for the individuals belonging to haplogroup Q1a3a1, as well as haplogroup I and the GenBank`s reference haplogroup R (Zuccarelli, Alechine et al 2011).…”

Section: Argentinean Populationmentioning

confidence: 99%

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Characterization of the AZF region of the Y chromosome in Native American haplogroup Q

Alechine¹,

Schempp²,

Corach³

2016

JOSHA

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JOSHA is a service that helps scholars, researchers, and students discover, use, and build upon a wide range of content MASTER THESISUNIVERSITY RESUMEN EN ESPAÑOLEl cromosoma Y humano, debido a sus características haploides, a la falta de recombinación y a su herencia uniparental por vía paterna, lleva en su secuencia la historia de su linaje. En reproducción masculina, se identificó la región AZF como responsable de la regulación de la espermatogénesis.Específicamente, la región AZFc abarca el 60% de las microdeleciones descriptas y su deleción completa es la causa genética más frecuente de infertilidad masculina. Sin embargo, las funciones específicas de los genes localizados en la región AZFc aún son poco claras. Genes localizados en esta región, como DAZ (Deleted in azoospermia) y CDY (Chromodomain protein Y), cumplen funciones importantes en la espermatogénesis, sin embargo el efecto de su deleción sobre la fertilidad no es igual en todos los individuos.Numerosos estudios indican que la presencia de ciertas microdeleciones en la región AZFc está relacionada con infertilidad masculina en determinadas poblaciones, mientras que las mismas deleciones no afectan la fertilidad en otras. Esto podría indicar que existen factores presentes en determinados haplogrupos del cromosoma Y que predisponen o protegen contra la infertilidad en presencia de las mismas microdeleciones. La hipótesis de la presente Tesis de Maestría es que individuos pertenecientes al haplogrupoNativo Americano Q1a3a1 podrían presentar polimorfismos estructurales en la región AZF del cromosoma Y sin signos de fertilidad disminuida. El objetivo de la misma es caracterizar el cromosoma Y de individuos de origen Nativo Americano pertenecientes al Hg Q1a3a1 para identificar posibles microdeleciones en la región AZFc y variaciones en el número de copias de los genes de CDY y DAZ, en hombres fértiles.

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“…The study was approved by the ethics committee of the Hospital de Clínicas José de San Martín, University of Buenos Aires, Argentina. The genetic ancestry of both patients was investigated using Realtime PCR- HRM [4] and SNaPShot ® followed by STRUCTURE 2.3.4 [5]. Case 1’s mitochondrial gene pool indicated Native American origin (mtDNA Haplogroup C, Y – Haplogroup R1b1a2) whilst autosomal ancestry information markers indicated a strong European ethnicity (99.2%).…”

Section: Dear Sirmentioning

confidence: 99%