Literature DB >> 20082090

Software for Y-haplogroup predictions: a word of caution.

Marina Muzzio1, Virginia Ramallo, Josefina M B Motti, Maria R Santos, Jorge S López Camelo, Graciela Bailliet.   

Abstract

The development of online software designed for genetic studies has been exponentially growing, providing numerous benefits to the scientific community. However, they should be used with care, since some require adjustments. The efficiency of two programs for haplogroup prediction was tested with 119 samples of known haplotypes and haplogroups from Argentine populations. Quantitative estimates of the predictive quality of both software systems were computed with the uncertainty coefficient; and sensitivity, specificity, positive, and negative likelihood ratios were also calculated to assert the reliability of both programs, showing high probabilities of assigning an incorrect haplogroup.

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Year:  2010        PMID： 20082090     DOI： 10.1007/s00414-009-0404-1

Source DB:  PubMed          Journal:  Int J Legal Med        ISSN： 0937-9827            Impact factor:   2.686


  18 in total

1.  Correlation between molecular and conventional genealogies in Aicuña: a rural population from Northwestern Argentina.

Authors:  G Bailliet; E E Castilla; J P Adams; I M Orioli; V L Martínez-Marignac; S M Richard; N O Bianchi
Journal:  Hum Hered       Date:  2001       Impact factor: 0.444

2.  A nomenclature system for the tree of human Y-chromosomal binary haplogroups.

Authors: 
Journal:  Genome Res       Date:  2002-02       Impact factor: 9.043

3.  Excavating Y-chromosome haplotype strata in Anatolia.

Authors:  Cengiz Cinnioğlu; Roy King; Toomas Kivisild; Ersi Kalfoğlu; Sevil Atasoy; Gianpiero L Cavalleri; Anita S Lillie; Charles C Roseman; Alice A Lin; Kristina Prince; Peter J Oefner; Peidong Shen; Ornella Semino; L Luca Cavalli-Sforza; Peter A Underhill
Journal:  Hum Genet       Date:  2003-10-29       Impact factor: 4.132

4.  Gender bias in the multiethnic genetic composition of central Argentina.

Authors:  A Salas; J C Jaime; V Álvarez-Iglesias; Á Carracedo
Journal:  J Hum Genet       Date:  2008-06-17       Impact factor: 3.172

Review 5.  How to read a paper. Papers that report diagnostic or screening tests.

Authors:  T Greenhalgh
Journal:  BMJ       Date:  1997-08-30

6.  Evaluation of Y-chromosomal STRs: a multicenter study.

Authors:  M Kayser; A Caglià; D Corach; N Fretwell; C Gehrig; G Graziosi; F Heidorn; S Herrmann; B Herzog; M Hidding; K Honda; M Jobling; M Krawczak; K Leim; S Meuser; E Meyer; W Oesterreich; A Pandya; W Parson; G Penacino; A Perez-Lezaun; A Piccinini; M Prinz; C Schmitt; L Roewer
Journal:  Int J Legal Med       Date:  1997       Impact factor: 2.686

7.  Chromosome Y microsatellites: population genetic and evolutionary aspects.

Authors:  P de Knijff; M Kayser; A Caglià; D Corach; N Fretwell; C Gehrig; G Graziosi; F Heidorn; S Herrmann; B Herzog; M Hidding; K Honda; M Jobling; M Krawczak; K Leim; S Meuser; E Meyer; W Oesterreich; A Pandya; W Parson; G Penacino; A Perez-Lezaun; A Piccinini; M Prinz; L Roewer
Journal:  Int J Legal Med       Date:  1997       Impact factor: 2.686

8.  Contrasting patterns of Y chromosome variation in Ashkenazi Jewish and host non-Jewish European populations.

Authors:  Doron M Behar; Daniel Garrigan; Matthew E Kaplan; Zahra Mobasher; Dror Rosengarten; Tatiana M Karafet; Lluis Quintana-Murci; Harry Ostrer; Karl Skorecki; Michael F Hammer
Journal:  Hum Genet       Date:  2004-01-22       Impact factor: 4.132

9.  Machine-learning approaches for classifying haplogroup from Y chromosome STR data.

Authors:  Joseph Schlecht; Matthew E Kaplan; Kobus Barnard; Tatiana Karafet; Michael F Hammer; Nirav C Merchant
Journal:  PLoS Comput Biol       Date:  2008-06-13       Impact factor: 4.475

10.  Y-chromosomal diversity in Lebanon is structured by recent historical events.

Authors:  Pierre A Zalloua; Yali Xue; Jade Khalife; Nadine Makhoul; Labib Debiane; Daniel E Platt; Ajay K Royyuru; Rene J Herrera; David F Soria Hernanz; Jason Blue-Smith; R Spencer Wells; David Comas; Jaume Bertranpetit; Chris Tyler-Smith
Journal:  Am J Hum Genet       Date:  2008-03-27       Impact factor: 11.025
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  9 in total

1.  Charting the Y-chromosome ancestry of present-day Argentinean Mennonites.

Authors:  Ulises Toscanini; Francesca Brisighelli; Cintia Llull; Gabriela Berardi; Andrea Gómez; Fernando Andreatta; Jacobo Pardo-Seco; Alberto Gómez-Carballa; Federico Martinón-Torres; Vanesa Álvarez-Iglesias; Antonio Salas
Journal:  J Hum Genet       Date:  2016-02-04       Impact factor: 3.172

2.  Demand for larger Y-STR reference databases in ethnic melting-pot countries: Argentina as a test case.

Authors:  Mariela Caputo; A Sala; D Corach
Journal:  Int J Legal Med       Date:  2019-02-09       Impact factor: 2.686

3.  Y-DNA genetic evidence reveals several different ancient origins in the Brahmin population.

Authors:  David G Mahal
Journal:  Mol Genet Genomics       Date:  2020-09-25       Impact factor: 3.291

4.  Croatian national reference Y-STR haplotype database.

Authors:  Gordan Mršić; Branka Gršković; Andro Vrdoljak; Maja Popović; Ivica Valpotić; Šimun Anđelinović; Vlastimil Stenzl; Edvard Ehler; Ludvik Urban; Gordana Lacković; Peter Underhill; Dragan Primorac
Journal:  Mol Biol Rep       Date:  2012-03-06       Impact factor: 2.316

5.  Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe.

Authors:  Edvard Ehler; Daniel Vane; Vlastimil Stenzl; Václav Vancata
Journal:  Croat Med J       Date:  2011-06       Impact factor: 1.351

6.  Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin.

Authors:  Jada Benn Torres; Miguel G Vilar; Gabriel A Torres; Jill B Gaieski; Ricardo Bharath Hernandez; Zoila E Browne; Marlon Stevenson; Wendell Walters; Theodore G Schurr
Journal:  PLoS One       Date:  2015-10-08       Impact factor: 3.240

7.  The Geographic Origins of Ethnic Groups in the Indian Subcontinent: Exploring Ancient Footprints with Y-DNA Haplogroups.

Authors:  David G Mahal; Ianis G Matsoukas
Journal:  Front Genet       Date:  2018-01-23       Impact factor: 4.599

8.  Population structure in Argentina.

Authors:  Marina Muzzio; Josefina M B Motti; Paula B Paz Sepulveda; Muh-Ching Yee; Thomas Cooke; María R Santos; Virginia Ramallo; Emma L Alfaro; Jose E Dipierri; Graciela Bailliet; Claudio M Bravi; Carlos D Bustamante; Eimear E Kenny
Journal:  PLoS One       Date:  2018-05-01       Impact factor: 3.240

9.  Y-STR Haplogroup Diversity in the Jat Population Reveals Several Different Ancient Origins.

Authors:  David G Mahal; Ianis G Matsoukas
Journal:  Front Genet       Date:  2017-09-20       Impact factor: 4.599
  9 in total

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