Skip to main content
Erschienen in: International Journal of Legal Medicine 1/2019

21.03.2018 | Short Communication

StatsX v2.0: the interactive graphical software for population statistics on X-STR

verfasst von: Yubo Lang, Fei Guo, Qingshan Niu

Erschienen in: International Journal of Legal Medicine | Ausgabe 1/2019

Einloggen, um Zugang zu erhalten

Abstract

StatsX (Statistics for X-STR) v2.0 is developed to facilitate the workflow for analysis of population data on X-chromosomal short tandem repeat (X-STR) marker. The interactive graphical and installable software can estimate allele/haplotype frequencies from female, male, and pooled samples and calculate forensic parameters by importing a single file. In addition, it is able to filter out the invalid raw data and export a series of pre-formatted Arlequin input files that are directly used for testing the significance of the Hardy–Weinberg equilibrium (HWE), linkage disequilibrium (LD), and gender differentiation. As expected, all results of frequencies and forensic parameters can be saved as EXCEL workbooks and also plotted as bar or line graphs. Further, full concordance was obtained by recalculating frequencies and forensic parameters with other established software from a published Han Chinese population.
Anhänge
Nur mit Berechtigung zugänglich
Literatur
1.
Zurück zum Zitat Diegoli TM (2015) Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 18:140–151CrossRefPubMed Diegoli TM (2015) Forensic typing of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 18:140–151CrossRefPubMed
2.
Zurück zum Zitat Qiagen (2015) Investigator® Argus X-12 QS handbook. Qiagen, Hilden Qiagen (2015) Investigator® Argus X-12 QS handbook. Qiagen, Hilden
3.
Zurück zum Zitat Sun K, Zhao S, Tian H, Zhang S, Li C (2013) Development of the 16 X-STR loci typing system and genetic analysis in a Shanghai Han population from China. Electrophoresis 34:3008–3015PubMed Sun K, Zhao S, Tian H, Zhang S, Li C (2013) Development of the 16 X-STR loci typing system and genetic analysis in a Shanghai Han population from China. Electrophoresis 34:3008–3015PubMed
4.
Zurück zum Zitat Yang X, Wu W, Chen L, Liu C, Zhang X, Chen L, Feng X, Wang H, Liu C (2016) Development of the 19 X-STR loci multiplex system and genetic analysis of a Zhejiang Han population in China. Electrophoresis 37:2260–2272CrossRefPubMed Yang X, Wu W, Chen L, Liu C, Zhang X, Chen L, Feng X, Wang H, Liu C (2016) Development of the 19 X-STR loci multiplex system and genetic analysis of a Zhejiang Han population in China. Electrophoresis 37:2260–2272CrossRefPubMed
5.
Zurück zum Zitat Gusmão L, Sánchez-Diz P, Alves C, Gomes I, Zarrabeitia MT, Abovich M, Atmetlla I, Bobillo C, Bravo L, Builes J, Cainé L, Calvo R, Carvalho E, Carvalho M, Cicarelli R, Catelli L, Corach D, Espinoza M, García O, Malaghini M, Martins J, Pinheiro F, João Porto M, Raimondi E, Riancho JA, Rodríguez A, Rodríguez A, Rodríguez Cardozo B, Schneider V, Silva S, Tavares C, Toscanini U, Vullo C, Whittle M, Yurrebaso I, Carracedo A, Amorim A (2009) A GEP-ISFG collaborative study on the optimization of an X-STR Decaplex: data on 15 Iberian and Latin American populations. Int J Legal Med 123:227–234CrossRefPubMed Gusmão L, Sánchez-Diz P, Alves C, Gomes I, Zarrabeitia MT, Abovich M, Atmetlla I, Bobillo C, Bravo L, Builes J, Cainé L, Calvo R, Carvalho E, Carvalho M, Cicarelli R, Catelli L, Corach D, Espinoza M, García O, Malaghini M, Martins J, Pinheiro F, João Porto M, Raimondi E, Riancho JA, Rodríguez A, Rodríguez A, Rodríguez Cardozo B, Schneider V, Silva S, Tavares C, Toscanini U, Vullo C, Whittle M, Yurrebaso I, Carracedo A, Amorim A (2009) A GEP-ISFG collaborative study on the optimization of an X-STR Decaplex: data on 15 Iberian and Latin American populations. Int J Legal Med 123:227–234CrossRefPubMed
6.
Zurück zum Zitat Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and windows. Mol Ecol Resour 10:564–567CrossRefPubMed Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and windows. Mol Ecol Resour 10:564–567CrossRefPubMed
7.
Zurück zum Zitat Szibor R, Hering S, Edelmann J (2006) A new Web site compiling forensic chromosome X research is now online. Int J Legal Med 120:252–254CrossRefPubMed Szibor R, Hering S, Edelmann J (2006) A new Web site compiling forensic chromosome X research is now online. Int J Legal Med 120:252–254CrossRefPubMed
8.
Zurück zum Zitat Guo F (2017) Population genetic data for 12 X-STR loci in the Northern Han Chinese and StatsX package as tools for population statistics on X-STR. Forensic Sci Int Genet 26:e1–e8CrossRefPubMed Guo F (2017) Population genetic data for 12 X-STR loci in the Northern Han Chinese and StatsX package as tools for population statistics on X-STR. Forensic Sci Int Genet 26:e1–e8CrossRefPubMed
9.
Zurück zum Zitat Diegoli TM, Rohde H, Borowski S, Krawczak M, Coble MD, Nothnagel M (2016) Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization. Forensic Sci Int Genet 25:39–44CrossRefPubMed Diegoli TM, Rohde H, Borowski S, Krawczak M, Coble MD, Nothnagel M (2016) Genetic mapping of 15 human X chromosomal forensic short tandem repeat (STR) loci by means of multi-core parallelization. Forensic Sci Int Genet 25:39–44CrossRefPubMed
10.
Zurück zum Zitat Prieto-Fernández E, Núñez C, Baeta M, Jiménez-Moreno S, Martínez-Jarreta B, de Pancorbo MM (2016) Forensic Spanish allele and haplotype database for a 17 X-STR panel. Forensic Sci Int Genet 24:120–123CrossRefPubMed Prieto-Fernández E, Núñez C, Baeta M, Jiménez-Moreno S, Martínez-Jarreta B, de Pancorbo MM (2016) Forensic Spanish allele and haplotype database for a 17 X-STR panel. Forensic Sci Int Genet 24:120–123CrossRefPubMed
11.
Zurück zum Zitat Nothnagel M, Szibor R, Vollrath O, Augustin C, Edelmann J, Geppert M, Alves C, Gusmão L, Vennemann M, Hou Y, Immel UD, Inturri S, Luo H, Lutz-Bonengel S, Robino C, Roewer L, Rolf B, Sanft J, Shin KJ, Sim JE, Wiegand P, Winkler C, Krawczak M, Hering S (2012) Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome. Forensic Sci Int Genet 6:778–784CrossRefPubMed Nothnagel M, Szibor R, Vollrath O, Augustin C, Edelmann J, Geppert M, Alves C, Gusmão L, Vennemann M, Hou Y, Immel UD, Inturri S, Luo H, Lutz-Bonengel S, Robino C, Roewer L, Rolf B, Sanft J, Shin KJ, Sim JE, Wiegand P, Winkler C, Krawczak M, Hering S (2012) Collaborative genetic mapping of 12 forensic short tandem repeat (STR) loci on the human X chromosome. Forensic Sci Int Genet 6:778–784CrossRefPubMed
12.
Zurück zum Zitat Tillmar AO, Kling D, Butler JM, Parson W, Prinz M, Schneider PM, Egeland T, Gusmão L (2017) DNA Commission of the International Society for Forensic Genetics (ISFG): guidelines on the use of X-STRs in kinship analysis. Forensic Sci Int Genet 29:269–275CrossRefPubMed Tillmar AO, Kling D, Butler JM, Parson W, Prinz M, Schneider PM, Egeland T, Gusmão L (2017) DNA Commission of the International Society for Forensic Genetics (ISFG): guidelines on the use of X-STRs in kinship analysis. Forensic Sci Int Genet 29:269–275CrossRefPubMed
13.
Zurück zum Zitat Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkCrossRef Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkCrossRef
14.
Zurück zum Zitat Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12:241–253CrossRefPubMed Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12:241–253CrossRefPubMed
15.
Zurück zum Zitat Botstein D, White RI, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedPubMedCentral Botstein D, White RI, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedPubMedCentral
16.
Zurück zum Zitat Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci 43:1046–1049CrossRefPubMed Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci 43:1046–1049CrossRefPubMed
17.
Zurück zum Zitat Krüger J, Fuhrmann W, Lichte KH, Steffens C (1968) On the utilization of erythrocyte acid phosphatase polymorphism in paternity evaluation. Dtsch Z Gesamte Gerichtl Med 64:127–146PubMed Krüger J, Fuhrmann W, Lichte KH, Steffens C (1968) On the utilization of erythrocyte acid phosphatase polymorphism in paternity evaluation. Dtsch Z Gesamte Gerichtl Med 64:127–146PubMed
18.
Zurück zum Zitat Kishida T, Wang W, Fukuda M, Tamaki Y (1997) Duplex PCR of the Y-27H39 and HPRT loci with reference to Japanese population data on the HPRT locus. Nihon Hoigaku Zasshi 51:67–69PubMed Kishida T, Wang W, Fukuda M, Tamaki Y (1997) Duplex PCR of the Y-27H39 and HPRT loci with reference to Japanese population data on the HPRT locus. Nihon Hoigaku Zasshi 51:67–69PubMed
19.
Zurück zum Zitat Huston KA (1998) Statistical analysis of STR data. Profiles in DNA 1:14–15 Huston KA (1998) Statistical analysis of STR data. Profiles in DNA 1:14–15
20.
Zurück zum Zitat Guo F, Li J, Wei T, Ye Q, Chen Z (2017) Genetic variation of 17 autosomal STR loci in the Zhuang ethnic minority from Guangxi Zhuang Autonomous Region in the south of China. Forensic Sci Int Genet 28:e51–e52PubMed Guo F, Li J, Wei T, Ye Q, Chen Z (2017) Genetic variation of 17 autosomal STR loci in the Zhuang ethnic minority from Guangxi Zhuang Autonomous Region in the south of China. Forensic Sci Int Genet 28:e51–e52PubMed
Metadaten
Titel
StatsX v2.0: the interactive graphical software for population statistics on X-STR
verfasst von
Yubo Lang
Fei Guo
Qingshan Niu
Publikationsdatum
21.03.2018
Verlag
Springer Berlin Heidelberg
Erschienen in
International Journal of Legal Medicine / Ausgabe 1/2019
Print ISSN: 0937-9827
Elektronische ISSN: 1437-1596
DOI
https://doi.org/10.1007/s00414-018-1824-6

Weitere Artikel der Ausgabe 1/2019

International Journal of Legal Medicine 1/2019 Zur Ausgabe

Neu im Fachgebiet Rechtsmedizin