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Sökning: onr:"swepub:oai:DiVA.org:uu-423041" > Predicting haplogro...

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex) : Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

Bouakaze, Caroline (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Inst Natl Police Sci, Lab Police Sci Lyon, 31 Ave Franklin Roosevelt, F-69134 Ecully, France.
Delehelle, Franklin (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;UMR 5505 CNRS, REVA Unit, F-31400 Toulouse, France.;Univ Toulouse, Inst Rech Informat Toulouse, F-31400 Toulouse, France.
Saenz-Oyhereguy, Nancy (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
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Moreira, Andreia (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Schiavinato, Stephanie (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Croze, Myriam (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Ewha Womans Univ, Div EcoSci, Seoul, South Korea.
Delon, Solene (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Fortes-Lima, Cesar A. (författare)
Uppsala universitet,Människans evolution,UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Gibert, Morgane (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Bujan, Louis (författare)
Hop Paule de Viguier, Equipe Acceuil EA3694, 330 Ave Grande Bretagne,TSA 70034, F-31059 Toulouse 9, France.
Huyghe, Eric (författare)
Hop Paule de Viguier, Equipe Acceuil EA3694, 330 Ave Grande Bretagne,TSA 70034, F-31059 Toulouse 9, France.
Bellis, Gil (författare)
INED Inst Natl Etud Demog, 133 Blvd Davout, F-75980 Paris 20, France.
Calderon, Rosario (författare)
Univ Complutense Madrid, Fac Biol, Dept Biodivers Ecol & Evolut, Madrid 28040, Spain.
Lucia Hernandez, Candela (författare)
Univ Complutense Madrid, Fac Biol, Dept Biodivers Ecol & Evolut, Madrid 28040, Spain.
Avendano-Tamayo, Efren (författare)
Inst Univ, Tecnol Antioquia, Grp Ciencias Basicas Aplicadas Tecnol Antioquia, Medellin 050034, Colombia.
Bedoya, Gabriel (författare)
Univ Antioquia Medellin Colombia, Inst Biol, GENMOL Genet Mol, Medellin, Colombia.
Salas, Antonio (författare)
Univ Santiago de Compostela, Hosp Clin Univ Santiago SERGAS, Fac Med,Unidade Xenet,GenPoB Res Grp, Inst Invest Sanitarias IDIS,Inst Ciencias Forense, Galicia, Spain.
Mazieres, Stephane (författare)
Aix Marseille Univ, ADES, EFS, CNRS, Marseille, France.
Charioni, Jacques (författare)
Aix Marseille Univ, ADES, EFS, CNRS, Marseille, France.;Etab Francais Sang PACA Corse, Marseille, France.
Migot-Nabias, Florence (författare)
Univ Paris, MERIT, IRD, F-75006 Paris, France.
Ruiz-Linares, Andres (författare)
Aix Marseille Univ, ADES, EFS, CNRS, Marseille, France.;Fudan Univ, Sch Life Sci, Key Lab Contemporary Anthropol, Minist Educ, Shanghai, Peoples R China.
Dugoujon, Jean-Michel (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Theves, Catherine (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Mollereau-Manaute, Catherine (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
Nous, Camille (författare)
CNRS, Lab Cogitamous, F-31000 Toulouse, France.;Univ Toulouse III, F-31000 Toulouse, France.
Poulet, Nicolas (författare)
Pole Ecohydraul AFB IMT, Allee Pr Camille Soula, F-31400 Toulouse, France.
King, Turi (författare)
Univ Leicester, Dept Genet, Leicester, Leics, England.
D'Amato, Maria Eugenia (författare)
Univ Western Cape, Fac Nat Sci, Dept Biotechnol, Forens DNA Lab, Cape Town, South Africa.
Balaresque, Patricia (författare)
UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.
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UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Inst Natl Police Sci, Lab Police Sci Lyon, 31 Ave Franklin Roosevelt, F-69134 Ecully, France. UMR5288 CNRS, Lab Anthropol Mol & Imagerie Synth AMIS, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;Univ Toulouse III, 37 Allees Jules Guesde, F-31073 Toulouse 3, France.;UMR 5505 CNRS, REVA Unit, F-31400 Toulouse, France.;Univ Toulouse, Inst Rech Informat Toulouse, F-31400 Toulouse, France. (creator_code:org_t)
Elsevier BV, 2020
2020
Engelska.
Ingår i: Forensic Science International. - : Elsevier BV. - 1872-4973 .- 1878-0326. ; 48
Relaterad länk:
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https://urn.kb.se/re...
https://doi.org/10.1...
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  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
Stäng  
  • We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.

Ämnesord

NATURVETENSKAP  -- Biologi -- Genetik (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Genetics (hsv//eng)

Nyckelord

Y-STR
Machine learning
Assignation accuracy and haplogroup prediction (Hg prediction)
Incremental mutation rates

Publikations- och innehållstyp

ref (ämneskategori)
art (ämneskategori)

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