Publications by authors named "Denilce Sumita"

5 Publications

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Paternal and maternal mutations in X-STRs: A GHEP-ISFG collaborative study.

Forensic Sci Int Genet 2020 05 5;46:102258. Epub 2020 Feb 5.

Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Brazil.

The GHEP-ISFG organized a collaborative study to estimate mutation rates for the markers included in the Investigator Argus X-12 QS kit Qiagen. A total of 16 laboratories gathered data from 1,612 father/mother/daughter trios, which were used to estimate both maternal and paternal mutation rates, when pooled together with other already published data. Data on fathers and mothers' age at the time of birth of the daughter were also available for ∼93 % of the cases. Population analyses were computed considering the genetic information of a subset of 1,327 unrelated daughters, corresponding to 2,654 haplotypes from residents in several regions of five countries: Argentina, Brazil, Ecuador, Portugal and Spain. Genetic differentiation analyses between the population samples from the same country did not reveal signs of significant stratification, although results from Hardy-Weinberg and linkage disequilibrium tests indicated the need of larger studies for Ecuador and Brazilian populations. The high genetic diversity of the markers resulted in a large number of haplotype combinations, showing the need of huge databases for reliable estimates of their frequencies. It should also be noted the high number of new alleles found, many of them not included in the allelic ladders provided with the kit, as very diverse populations were analyzed. The overall estimates for locus specific average mutation rates varied between 7.5E-04 (for DXS7423) and 1.1E-02 (for DXS10135), the latter being a troublesome figure for kinship analyses. Most of the found mutations (∼92 %) are compatible with the gain or loss of a single repeat. Paternal mutation rates showed to be 5.2 times higher than maternal ones. We also found that older fathers were more prone to transmit mutated alleles, having this trend not been observed in the case of the mothers.
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http://dx.doi.org/10.1016/j.fsigen.2020.102258DOI Listing
May 2020

Results of a collaborative study on DNA identification of aged bone samples.

Croat Med J 2017 Jun;58(3):203-213

Daniel Vanek, Forensic DNA Service, Budinova 2, 180 81 Prague 8, Czech Republic,

Aim: A collaborative exercise with several institutes was organized by the Forensic DNA Service (FDNAS) and the Institute of the Legal Medicine, 2nd Faculty of Medicine, Charles University in Prague, Czech Republic, with the aim to test performance of different laboratories carrying out DNA analysis of relatively old bone samples.

Methods: Eighteen laboratories participating in the collaborative exercise were asked to perform DNA typing of two samples of bone powder. Two bone samples provided by the National Museum and the Institute of Archaelogy in Prague, Czech Republic, came from archeological excavations and were estimated to be approximately 150 and 400 years old. The methods of genetic characterization including autosomal, gonosomal, and mitochondrial markers was selected solely at the discretion of the participating laboratory.

Results: Although the participating laboratories used different extraction and amplification strategies, concordant results were obtained from the relatively intact 150 years old bone sample. Typing was more problematic with the analysis of the 400 years old bone sample due to poorer quality.

Conclusion: The laboratories performing identification DNA analysis of bone and teeth samples should regularly test their ability to correctly perform DNA-based identification on bone samples containing degraded DNA and potential inhibitors and demonstrate that risk of contamination is minimized.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470125PMC
http://dx.doi.org/10.3325/cmj.2017.58.203DOI Listing
June 2017

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

Authors:
Josephine Purps Sabine Siegert Sascha Willuweit Marion Nagy Cíntia Alves Renato Salazar Sheila M T Angustia Lorna H Santos Katja Anslinger Birgit Bayer Qasim Ayub Wei Wei Yali Xue Chris Tyler-Smith Miriam Baeta Bafalluy Begoña Martínez-Jarreta Balazs Egyed Beate Balitzki Sibylle Tschumi David Ballard Denise Syndercombe Court Xinia Barrantes Gerhard Bäßler Tina Wiest Burkhard Berger Harald Niederstätter Walther Parson Carey Davis Bruce Budowle Helen Burri Urs Borer Christoph Koller Elizeu F Carvalho Patricia M Domingues Wafaa Takash Chamoun Michael D Coble Carolyn R Hill Daniel Corach Mariela Caputo Maria E D'Amato Sean Davison Ronny Decorte Maarten H D Larmuseau Claudio Ottoni Olga Rickards Di Lu Chengtao Jiang Tadeusz Dobosz Anna Jonkisz William E Frank Ivana Furac Christian Gehrig Vincent Castella Branka Grskovic Cordula Haas Jana Wobst Gavrilo Hadzic Katja Drobnic Katsuya Honda Yiping Hou Di Zhou Yan Li Shengping Hu Shenglan Chen Uta-Dorothee Immel Rüdiger Lessig Zlatko Jakovski Tanja Ilievska Anja E Klann Cristina Cano García Peter de Knijff Thirsa Kraaijenbrink Aikaterini Kondili Penelope Miniati Maria Vouropoulou Lejla Kovacevic Damir Marjanovic Iris Lindner Issam Mansour Mouayyad Al-Azem Ansar El Andari Miguel Marino Sandra Furfuro Laura Locarno Pablo Martín Gracia M Luque Antonio Alonso Luís Souto Miranda Helena Moreira Natsuko Mizuno Yasuki Iwashima Rodrigo S Moura Neto Tatiana L S Nogueira Rosane Silva Marina Nastainczyk-Wulf Jeanett Edelmann Michael Kohl Shengjie Nie Xianping Wang Baowen Cheng Carolina Núñez Marian Martínez de Pancorbo Jill K Olofsson Niels Morling Valerio Onofri Adriano Tagliabracci Horolma Pamjav Antonia Volgyi Gusztav Barany Ryszard Pawlowski Agnieszka Maciejewska Susi Pelotti Witold Pepinski Monica Abreu-Glowacka Christopher Phillips Jorge Cárdenas Danel Rey-Gonzalez Antonio Salas Francesca Brisighelli Cristian Capelli Ulises Toscanini Andrea Piccinini Marilidia Piglionica Stefania L Baldassarra Rafal Ploski Magdalena Konarzewska Emila Jastrzebska Carlo Robino Antti Sajantila Jukka U Palo Evelyn Guevara Jazelyn Salvador Maria Corazon De Ungria Jae Joseph Russell Rodriguez Ulrike Schmidt Nicola Schlauderer Pekka Saukko Peter M Schneider Miriam Sirker Kyoung-Jin Shin Yu Na Oh Iulia Skitsa Alexandra Ampati Tobi-Gail Smith Lina Solis de Calvit Vlastimil Stenzl Thomas Capal Andreas Tillmar Helena Nilsson Stefania Turrina Domenico De Leo Andrea Verzeletti Venusia Cortellini Jon H Wetton Gareth M Gwynne Mark A Jobling Martin R Whittle Denilce R Sumita Paulina Wolańska-Nowak Rita Y Y Yong Michael Krawczak Michael Nothnagel Lutz Roewer

Forensic Sci Int Genet 2014 Sep 28;12:12-23. Epub 2014 Apr 28.

Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany. Electronic address:

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.
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http://dx.doi.org/10.1016/j.fsigen.2014.04.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127773PMC
September 2014

Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome.

PLoS One 2010 Jun 4;5(6):e10947. Epub 2010 Jun 4.

Laboratório de Genética Molecular do Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.

Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 22 X-linked genes, including XIST, using 27 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this analysis indicated heterogeneous maintenance of gene silencing along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010947PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881032PMC
June 2010

Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study.

Int J Legal Med 2008 Nov 24;122(6):529-33. Epub 2008 Jul 24.

University of Santiago de Compostela, C/San Francisco, A Coruña, Spain.

A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25 x 10(-4) (95% CI 0.05 x 10(-3)-1.53 x 10(-3)) at DYS438 and 6.36 x 10(-3) (95% CI 2.75 x 10(-3)-12.49 x 10(-3)) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice.
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http://dx.doi.org/10.1007/s00414-008-0265-zDOI Listing
November 2008