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8. The Utilization of the SaLux19-Based Loop-Mediated Isothermal Amplification (LAMP) Assay for the Rapid and Sensitive Identification of Minute Amounts of a Biological Specimen.

Author

Ruszova, Ema, Vanek, Daniel, Stühmer, Walter, Khaznadar, Ziad, and Subhashini, Nidhi

Subjects
*BIOLOGICAL specimens, *LOOP-mediated isothermal amplification, *WILD boar, *NUCLEIC acids, *BIOLOGICAL assay, *BIOMATERIALS
Abstract

Our research has developed a highly sensitive and simple assay to detect small amounts of animal and human biological material in less than 40 min. The handheld SaLux19 device developed at the Max Planck Institute of Experimental Medicine in Göttingen, Germany, was used to validate our concept. The proposed system uses isothermal amplification of DNA in a rapid assay format. Our results show that the assay can detect Sus scrofa nucleic acids with very high sensitivity and specificity. This detection system has potential for forensic scenarios. [ABSTRACT FROM AUTHOR]

Published
2024
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26. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Author

Ballantyne, Kaye N., Ralf, Arwin, Aboukhalid, Rachid, Achakzai, Niaz M., Anjos, Maria J., Ayub, Qasim, Balažic, Jože, Ballantyne, Jack, Ballard, David J., Berger, Burkhard, Bobillo, Cecilia, Bouabdellah, Mehdi, Burri, Helen, Capal, Tomas, Caratti, Stefano, Cárdenas, Jorge, Cartault, François, Carvalho, Elizeu F., Carvalho, Monica, Cheng, Baowen, Coble, Michael D., Comas, David, Corach, Daniel, DʼAmato, Maria E., Davison, Sean, de Knijff, Peter, De Ungria, Maria Corazon A., Decorte, Ronny, Dobosz, Tadeusz, Dupuy, Berit M., Elmrghni, Samir, Gliwiński, Mateusz, Gomes, Sara C., Grol, Laurens, Haas, Cordula, Hanson, Erin, Henke, Jürgen, Henke, Lotte, Herrera-Rodríguez, Fabiola, Hill, Carolyn R., Holmlund, Gunilla, Honda, Katsuya, Immel, Uta-Dorothee, Inokuchi, Shota, Jobling, Mark A., Kaddura, Mahmoud, Kim, Jong S., Kim, Soon H., Kim, Wook, King, Turi E., Klausriegler, Eva, Kling, Daniel, Kovačević, Lejla, Kovatsi, Leda, Krajewski, Paweł, Kravchenko, Sergey, Larmuseau, Maarten H. D., Lee, Eun Young, Lessig, Ruediger, Livshits, Ludmila A., Marjanović, Damir, Minarik, Marek, Mizuno, Natsuko, Moreira, Helena, Morling, Niels, Mukherjee, Meeta, Munier, Patrick, Nagaraju, Javaregowda, Neuhuber, Franz, Nie, Shengjie, Nilasitsataporn, Premlaphat, Nishi, Takeki, Oh, Hye H., Olofsson, Jill, Onofri, Valerio, Palo, Jukka U., Pamjav, Horolma, Parson, Walther, Petlach, Michal, Phillips, Christopher, Ploski, Rafal, Prasad, Samayamantri P. R., Primorac, Dragan, Purnomo, Gludhug A., Purps, Josephine, Rangel-Villalobos, Hector, Rębała, Krzysztof, Rerkamnuaychoke, Budsaba, Gonzalez, Danel Rey, Robino, Carlo, Roewer, Lutz, Rosa, Alexandra, Sajantila, Antti, Sala, Andrea, Salvador, Jazelyn M., Sanz, Paula, Schmitt, Cornelia, Sharma, Anil K., Silva, Dayse A., Shin, Kyoung-Jin, Sijen, Titia, Sirker, Miriam, Siváková, Daniela, Škaro, Vedrana, Solano-Matamoros, Carlos, Souto, Luis, Stenzl, Vlastimil, Sudoyo, Herawati, Syndercombe-Court, Denise, Tagliabracci, Adriano, Taylor, Duncan, Tillmar, Andreas, Tsybovsky, Iosif S., Tyler-Smith, Chris, van der Gaag, Kristiaan J., Vanek, Daniel, Völgyi, Antónia, Ward, Denise, Willemse, Patricia, Yap, Eric P.H., Yong, Rita Y.Y., Zupanič Pajnič, Irena, and Kayser, Manfred

Published
2014
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28. STR analysis of artificially degraded DNA--results of a collaborative European exercise.

Author

Schneider, Peter M., Bender, Klaus, Mayr, Wolfgang R., Parson, Walther, Hoste, Bernadette, Decorte, Ronny, Cordonnier, Jan, Vanek, Daniel, Morling, Niels, Karjalainen, Matti, Carlotti, C. Marie-Paule, Sabatier, Myriam, Hohoff, Carsten, Schmitter, Hermann, Pflug, Werner, Wenzel, Rainer, Patzelt, Dieter, Lessig, Rudiger, Dobrowolski, Peter, O'Donnell, Geraldine, Garafano, Luciano, Dobosz, Marina, de Knijff, Peter, Mevag, Bente, Pawlowski, Ryszard, Gusmao, Leonor, Vide, Maria Conceicao, Alonso, Antonio, Fernandez, Oscar Garcia, Nicolas, Pilar Sanz, Kihlgreen, Ann, Bar, Walter, Meier, Verena, Teyssier, Anne, Coquoz, Raphael, Brandt, Conxita, Germann, Ursula, Gill, Peter, Hallett, Justine, and Greenhalgh, Matthew

Subjects
Polymerase chain reaction -- Analysis -- Research, Decomposition (Chemistry) -- Analysis -- Research, Allelomorphism -- Research -- Analysis
Abstract

Abstract Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. [...]

Published
2004

34. Croatian Medical Journal / Results of a collaborative study on DNA identification of aged bone samples

Author

Vanek, Daniel, Budowle, Bruce, Dubska-Votrubova, Jitka, Ambers, Angie, Frolik, Jan, Pospisek, Martin, Al Afeefi, Ahmed Anwar, Al Hosani, Khalid Ismaeil, Allen, Marie, Al Naimi, Khudooma Saeed, Al Salafi, Dina, Al Tayyari, Wafa Ali Rashid, Arguetaa, Wendy, Bottinelli, Michel, Bus, Magdalena M., Cemper-Kiesslich, Jan, Cepil, Olivier, De Cock, Greet, Desmyter, Stijn, El Amri, Hamid, El Ossmani, Hicham, Galdies, Ruth, and Grün, Sebastian

Abstract

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. (VLID)5344846

Published
2017
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35. Results of a collaborative study on DNA identification of aged bone samples

Author

Vanek, Daniel, primary, Budowle, Bruce, additional, Dubska-Votrubova, Jitka, additional, Ambers, Angie, additional, Frolik, Jan, additional, Pospisek, Martin, additional, Al Afeefi, Ahmed Anwar, additional, Al Hosani, Khalid Ismaeil, additional, Allen, Marie, additional, Al Naimi, Khudooma Saeed, additional, Al Salafi, Dina, additional, Al Tayyari, Wafa Ali Rashid, additional, Arguetaa, Wendy, additional, Bottinelli, Michel, additional, Bus, Magdalena M., additional, Cemper-Kiesslich, Jan, additional, Cepil, Olivier, additional, De Cock, Greet, additional, Desmyter, Stijn, additional, El Amri, Hamid, additional, El Ossmani, Hicham, additional, Galdies, Ruth, additional, Grün, Sebastian, additional, Guidet, Francois, additional, Hoefges, Anna, additional, Iancu, Cristian Bogdan, additional, Lotz, Petra, additional, Maresca, Alessandro, additional, Nagy, Marion, additional, Novotny, Jindrich, additional, Rachid, Hajar, additional, Rothe, Jessica, additional, Stenersen, Marguerethe, additional, Stephenson, Mishel, additional, Stevanovitch, Alain, additional, Strien, Juliane, additional, Sumita, Denilce R., additional, Vella, Joanna, additional, and Zander, Judith, additional

Published
2017
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36. Results of a collaborative study on DNA identification of aged bone samples

Author

Vanek, Daniel, Budowle, Bruce, Dubska-Votrubova, Jitka, Ambers, Angie, Frolik, Jan, Pospisek, Martin, Al Afeefi, Ahmed Anwar, Al Hosani, Khalid Ismaeil, Allen, Marie, Al Naimi, Khudooma Saeed, Al Salafi, Dina, Al Tayyari, Wafa Ali Rashid, Arguetaa, Wendy, Bottinelli, Michel, Bus, Magdalena M., Cemper-Kiesslich, Jan, Cepil, Olivier, De Cock, Greet, Desmyter, Stijn, El Amri, Hamid, El Ossmani, Hicham, Galdies, Ruth, Gruen, Sebastian, Guidet, Francois, Hoefges, Anna, Iancu, Cristian Bogdan, Lotz, Petra, Maresca, Alessandro, Nagy, Marion, Novotny, Jindrich, Rachid, Hajar, Rothe, Jessica, Stenersen, Marguerethe, Stephenson, Mishel, Stevanovitch, Alain, Strien, Juliane, Sumita, Denilce R., Vella, Joanna, Zander, Judith, Vanek, Daniel, Budowle, Bruce, Dubska-Votrubova, Jitka, Ambers, Angie, Frolik, Jan, Pospisek, Martin, Al Afeefi, Ahmed Anwar, Al Hosani, Khalid Ismaeil, Allen, Marie, Al Naimi, Khudooma Saeed, Al Salafi, Dina, Al Tayyari, Wafa Ali Rashid, Arguetaa, Wendy, Bottinelli, Michel, Bus, Magdalena M., Cemper-Kiesslich, Jan, Cepil, Olivier, De Cock, Greet, Desmyter, Stijn, El Amri, Hamid, El Ossmani, Hicham, Galdies, Ruth, Gruen, Sebastian, Guidet, Francois, Hoefges, Anna, Iancu, Cristian Bogdan, Lotz, Petra, Maresca, Alessandro, Nagy, Marion, Novotny, Jindrich, Rachid, Hajar, Rothe, Jessica, Stenersen, Marguerethe, Stephenson, Mishel, Stevanovitch, Alain, Strien, Juliane, Sumita, Denilce R., Vella, Joanna, and Zander, Judith

Abstract

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.

Published
2017
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37. Towards male individualization with rapidly mutating Y-chromosomal STRs

Author

Ballantyne, Kaye N, Ralf, Arwin, Aboukhalid, Rachid, Achakzai, Niaz M, Anjos, Maria J, Ayub, Qasim, Balažic, Jože, Ballantyne, Jack, Ballard, David J, Berger, Burkhard, Bobillo, Cecilia, Bouabdellah, Mehdi, Burri, Helen, Capal, Tomas, Caratti, Stefano, Cárdenas, Jorge, Cartault, François, Carvalho, Elizeu F, Carvalho, Monica, Cheng, Baowen, Coble, Michael D, Comas, David, Corach, Daniel, D'Amato, Maria E, Davison, Sean, de Knijff, Peter, De Ungria, Maria Corazon A, Decorte, Ronny, Dobosz, Tadeusz, Dupuy, Berit M, Elmrghni, Samir, Gliwiński, Mateusz, Gomes, Sara C, Grol, Laurens, Haas, Cordula, Hanson, Erin, Henke, Jürgen, Henke, Lotte, Herrera-Rodríguez, Fabiola, Hill, Carolyn R, Holmlund, Gunilla, Honda, Katsuya, Immel, Uta-Dorothee, Inokuchi, Shota, Jobling, Mark A, Kaddura, Mahmoud, Kim, Jong S, Kim, Soon H, Kim, Wook, King, Turi E, Klausriegler, Eva, Kling, Daniel, Kovačević, Lejla, Kovatsi, Leda, Krajewski, Paweł, Kravchenko, Sergey, Larmuseau, Maarten H D, Lee, Eun Young, Lessig, Ruediger, Livshits, Ludmila A, Marjanović, Damir, Minarik, Marek, Mizuno, Natsuko, Moreira, Helena, Morling, Niels, Mukherjee, Meeta, Munier, Patrick, Nagaraju, Javaregowda, Neuhuber, Franz, Nie, Shengjie, Nilasitsataporn, Premlaphat, Nishi, Takeki, Oh, Hye H, Olofsson, Jill, Onofri, Valerio, Palo, Jukka U, Pamjav, Horolma, Parson, Walther, Petlach, Michal, Phillips, Christopher, Ploski, Rafal, Prasad, Samayamantri P R, Primorac, Dragan, Purnomo, Gludhug A, Purps, Josephine, Rangel-Villalobos, Hector, Rębała, Krzysztof, Rerkamnuaychoke, Budsaba, Gonzalez, Danel Rey, Robino, Carlo, Roewer, Lutz, Rosa, Alexandra, Sajantila, Antti, Sala, Andrea, Salvador, Jazelyn M, Sanz, Paula, Schmitt, Cornelia, Sharma, Anil K, Silva, Dayse A, Shin, Kyoung-Jin, Sijen, Titia, Sirker, Miriam, Siváková, Daniela, Skaro, Vedrana, Solano-Matamoros, Carlos, Souto, Luis, Stenzl, Vlastimil, Sudoyo, Herawati, Court, Denise Syndercombe, Tagliabracci, Adriano, Taylor, Duncan, Tillmar, Andreas, Tsybovsky, Iosif S, Tyler-Smith, Chris, van der Gaag, Kristiaan J, Vanek, Daniel, Völgyi, Antónia, Ward, Denise, Willemse, Patricia, Yap, Eric P H, Yong, Rita Y Y, Pajnič, Irena Zupanič, and Kayser, Manfred

Abstract

Relevant for various areas of human genetics, Y-chromosomal STRs (Y-STRs) are commonly used for testing close paternal relationships amongst individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly-mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99919-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% non-unique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). AMOVA revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 fathers/son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.

Published
2014
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39. Highly Effective DNA Extraction Method for Nuclear Short Tandem Repeat Testing of Skeletal Remains from Mass Graves

Author

Davoren, Jon, Vanek, Daniel, Konjhodzić, Rijad, Crews, John, Huffine, Edwin, and Parsons, Thomas J.

Subjects
Forensic Science, Forensic Anthropology, Humans, DNA, Bone and Bones, Microsatellite Repeats
Abstract

To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves.DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit.DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles.The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method.

Published
2007

40. Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats

Author

Ballantyne, Kaye N, Ralf, Arwin, Aboukhalid, Rachid, Achakzai, Niaz M, Anjos, Maria J, Ayub, Qasim, Balažic, Jože, Ballantyne, Jack, Ballard, David J, Berger, Burkhard, Bobillo, Cecilia, Bouabdellah, Mehdi, Burri, Helen, Capal, Tomas, Caratti, Stefano, Cárdenas, Jorge, Cartault, François, Carvalho, Elizeu F, Carvalho, Monica, Cheng, Baowen, Coble, Michael D, Comas, David, Corach, Daniel, D'Amato, Maria E, Davison, Sean, de Knijff, Peter, De Ungria, Maria Corazon A, Decorte, Ronny, Dobosz, Tadeusz, Dupuy, Berit M, Elmrghni, Samir, Gliwiński, Mateusz, Gomes, Sara C, Grol, Laurens, Haas, Cordula, Hanson, Erin, Henke, Jürgen, Henke, Lotte, Herrera-Rodríguez, Fabiola, Hill, Carolyn R, Holmlund, Gunilla, Honda, Katsuya, Immel, Uta-Dorothee, Inokuchi, Shota, Jobling, Mark A, Kaddura, Mahmoud, Kim, Jong S, Kim, Soon H, Kim, Wook, King, Turi E, Klausriegler, Eva, Kling, Daniel, Kovačević, Lejla, Kovatsi, Leda, Krajewski, Paweł, Kravchenko, Sergey, Larmuseau, Maarten H D, Lee, Eun Young, Lessig, Ruediger, Livshits, Ludmila A, Marjanović, Damir, Minarik, Marek, Mizuno, Natsuko, Moreira, Helena, Morling, Niels, Mukherjee, Meeta, Munier, Patrick, Nagaraju, Javaregowda, Neuhuber, Franz, Nie, Shengjie, Nilasitsataporn, Premlaphat, Nishi, Takeki, Oh, Hye H, Olofsson, Jill Katharina, Onofri, Valerio, Palo, Jukka U, Pamjav, Horolma, Parson, Walther, Petlach, Michal, Phillips, Christopher, Ploski, Rafal, Prasad, Samayamantri P R, Primorac, Dragan, Purnomo, Gludhug A, Purps, Josephine, Rangel-Villalobos, Hector, Rębała, Krzysztof, Rerkamnuaychoke, Budsaba, Gonzalez, Danel Rey, Robino, Carlo, Roewer, Lutz, Rosa, Alexandra, Sajantila, Antti, Sala, Andrea, Salvador, Jazelyn M, Sanz, Paula, Schmitt, Cornelia, Sharma, Anil K, Silva, Dayse A, Shin, Kyoung-Jin, Sijen, Titia, Sirker, Miriam, Siváková, Daniela, Skaro, Vedrana, Solano-Matamoros, Carlos, Souto, Luis, Stenzl, Vlastimil, Sudoyo, Herawati, Court, Denise Syndercombe, Tagliabracci, Adriano, Taylor, Duncan, Tillmar, Andreas, Tsybovsky, Iosif S, Tyler-Smith, Chris, van der Gaag, Kristiaan J, Vanek, Daniel, Völgyi, Antónia, Ward, Denise, Willemse, Patricia, Yap, Eric P H, Yong, Rita Y Y, Pajnič, Irena Zupanič, Kayser, Manfred, Ballantyne, Kaye N, Ralf, Arwin, Aboukhalid, Rachid, Achakzai, Niaz M, Anjos, Maria J, Ayub, Qasim, Balažic, Jože, Ballantyne, Jack, Ballard, David J, Berger, Burkhard, Bobillo, Cecilia, Bouabdellah, Mehdi, Burri, Helen, Capal, Tomas, Caratti, Stefano, Cárdenas, Jorge, Cartault, François, Carvalho, Elizeu F, Carvalho, Monica, Cheng, Baowen, Coble, Michael D, Comas, David, Corach, Daniel, D'Amato, Maria E, Davison, Sean, de Knijff, Peter, De Ungria, Maria Corazon A, Decorte, Ronny, Dobosz, Tadeusz, Dupuy, Berit M, Elmrghni, Samir, Gliwiński, Mateusz, Gomes, Sara C, Grol, Laurens, Haas, Cordula, Hanson, Erin, Henke, Jürgen, Henke, Lotte, Herrera-Rodríguez, Fabiola, Hill, Carolyn R, Holmlund, Gunilla, Honda, Katsuya, Immel, Uta-Dorothee, Inokuchi, Shota, Jobling, Mark A, Kaddura, Mahmoud, Kim, Jong S, Kim, Soon H, Kim, Wook, King, Turi E, Klausriegler, Eva, Kling, Daniel, Kovačević, Lejla, Kovatsi, Leda, Krajewski, Paweł, Kravchenko, Sergey, Larmuseau, Maarten H D, Lee, Eun Young, Lessig, Ruediger, Livshits, Ludmila A, Marjanović, Damir, Minarik, Marek, Mizuno, Natsuko, Moreira, Helena, Morling, Niels, Mukherjee, Meeta, Munier, Patrick, Nagaraju, Javaregowda, Neuhuber, Franz, Nie, Shengjie, Nilasitsataporn, Premlaphat, Nishi, Takeki, Oh, Hye H, Olofsson, Jill Katharina, Onofri, Valerio, Palo, Jukka U, Pamjav, Horolma, Parson, Walther, Petlach, Michal, Phillips, Christopher, Ploski, Rafal, Prasad, Samayamantri P R, Primorac, Dragan, Purnomo, Gludhug A, Purps, Josephine, Rangel-Villalobos, Hector, Rębała, Krzysztof, Rerkamnuaychoke, Budsaba, Gonzalez, Danel Rey, Robino, Carlo, Roewer, Lutz, Rosa, Alexandra, Sajantila, Antti, Sala, Andrea, Salvador, Jazelyn M, Sanz, Paula, Schmitt, Cornelia, Sharma, Anil K, Silva, Dayse A, Shin, Kyoung-Jin, Sijen, Titia, Sirker, Miriam, Siváková, Daniela, Skaro, Vedrana, Solano-Matamoros, Carlos, Souto, Luis, Stenzl, Vlastimil, Sudoyo, Herawati, Court, Denise Syndercombe, Tagliabracci, Adriano, Taylor, Duncan, Tillmar, Andreas, Tsybovsky, Iosif S, Tyler-Smith, Chris, van der Gaag, Kristiaan J, Vanek, Daniel, Völgyi, Antónia, Ward, Denise, Willemse, Patricia, Yap, Eric P H, Yong, Rita Y Y, Pajnič, Irena Zupanič, and Kayser, Manfred

Abstract

Relevant for various areas of human genetics, Y-chromosomal STRs (Y-STRs) are commonly used for testing close paternal relationships amongst individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly-mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99919-0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% non-unique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). AMOVA revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 fathers/son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database. This article is protected by copyright. All rights reserved.

Published
2014

41. STR analysis of artificially degraded DNA-results of a collaborative European exercise

Author

Schneider, Peter M, Bender, Klaus, Mayr, Wolfgang R, Parson, Walther, Hoste, Bernadette, Decorte, Ronny, Cordonnier, Jan, Vanek, Daniel, Morling, Niels, Karjalainen, Matti, Marie-Paule Carlotti, C, Sabatier, Myriam, Hohoff, Carsten, Schmitter, Hermann, Pflug, Werner, Wenzel, Rainer, Patzelt, Dieter, Lessig, Rüdiger, Dobrowolski, Peter, O'Donnell, Geraldine, Garafano, Luciano, Dobosz, Marina, De Knijff, Peter, Mevag, Bente, Pawlowski, Ryszard, Gusmão, Leonor, Conceicao Vide, Maria, Alonso Alonso, Antonio, García Fernández, Oscar, Sanz Nicolás, Pilar, Kihlgreen, Ann, Bär, Walter, Meier, Verena, Teyssier, Anne, Coquoz, Raphael, Brandt, Conxita, Germann, Ursula, Gill, Peter, Hallett, Justine, Greenhalgh, Matthew, Schneider, Peter M, Bender, Klaus, Mayr, Wolfgang R, Parson, Walther, Hoste, Bernadette, Decorte, Ronny, Cordonnier, Jan, Vanek, Daniel, Morling, Niels, Karjalainen, Matti, Marie-Paule Carlotti, C, Sabatier, Myriam, Hohoff, Carsten, Schmitter, Hermann, Pflug, Werner, Wenzel, Rainer, Patzelt, Dieter, Lessig, Rüdiger, Dobrowolski, Peter, O'Donnell, Geraldine, Garafano, Luciano, Dobosz, Marina, De Knijff, Peter, Mevag, Bente, Pawlowski, Ryszard, Gusmão, Leonor, Conceicao Vide, Maria, Alonso Alonso, Antonio, García Fernández, Oscar, Sanz Nicolás, Pilar, Kihlgreen, Ann, Bär, Walter, Meier, Verena, Teyssier, Anne, Coquoz, Raphael, Brandt, Conxita, Germann, Ursula, Gill, Peter, Hallett, Justine, and Greenhalgh, Matthew

Abstract

Udgivelsesdato: 2004-Jan-28, Degradation of human DNA extracted from forensic stains is, in most cases, the result of a natural process due to the exposure of the stain samples to the environment. Experiences with degraded DNA from casework samples show that every sample may exhibit different properties in this respect, and that it is difficult to systematically assess the performance of routinely used typing systems for the analysis of degraded DNA samples. Using a batch of artificially degraded DNA with an average fragment size of approx. 200 bp a collaborative exercise was carried out among 38 forensic laboratories from 17 European countries. The results were assessed according to correct allele detection, peak height and balance as well as the occurrence of artefacts. A number of common problems were identified based on these results such as strong peak imbalance in heterozygous genotypes for the larger short tandem repeat (STR) fragments after increased PCR cycle numbers, artefact signals and allelic drop-out. Based on the observations, strategies are discussed to overcome these problems. The strategies include careful balancing of the amount of template DNA and the PCR cycle numbers, the reaction volume and the amount of Taq polymerase. Furthermore, a careful evaluation of the results of the fragment analysis and of automated allele calling is necessary to identify the correct alleles and avoid artefacts.

Published
2004

46. Evaluation of 14 Ychromosomal Short Tandem Repeat Haplotype with Focus on DYS449, DYS456, and DYS458: Czech Population Sample.

Author

Ehler, Edvard, Marvan, Richard, and Vanek, Daniel

Subjects
*POLYMERASE chain reaction, *Y chromosome, *GENETIC polymorphisms, *POPULATION differentiation, *CHROMOSOME polymorphism, *POPULATION statistics
Abstract

Aim To evaluate the novel triplex polymerase chain reaction (PCR) assay for the analysis of polymorphic Y-chromosomal short tandem repeat loci (Y-STR). Methods A total of 14 Y-STR loci was analyzed. Allele frequencies for 3 tetrameric Y-STR loci (DYS449, DYS456, and DYS458) and extended haplotype loci typed by Y-PLEX™ 12 system were investigated in a sample of 50 unrelated healthy Czech male donors. We computed the relevant intra- population statistic parameters for our data (gene diversity, average gene diversity over loci, and mean number of pairwise differences) and compared our sample set with other Central European populations using RST pairwise genetic distance. Results We focused on the comparison of genetic diversity between the Y-STR extended haplotype loci and that of the 3 additional loci, and on the benefit of using DYS449, DYS456, and DYS458 in forensic and population genetics applications. Total gene diversity in our sample set was 0.998367 when using all 14 loci. Our data analysis revealed very high genetic diversity at DYS449 locus (0.876735), which surpasses even the diversity at DYS385a/ b (0.819592). Population comparison showed no difference between Czech, Bavarian, Austrian, and Saxon sample set. A minor difference was found between Czech and Polish sample set. Conclusion Typing of 3 Y-chromosomal microsatellite polymorphisms may provide a useful complement to already established sets of Y-STRs. [ABSTRACT FROM AUTHOR]

Published
2010
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47. Highly effective DNA extraction method for nuclear short tandem repeat testing of skeletal remains from mass graves.

Author

Davoren J, Vanek D, Konjhodzić R, Crews J, Huffine E, and Parsons TJ

Subjects
Humans, Bone and Bones chemistry, DNA isolation & purification, Forensic Anthropology methods, Microsatellite Repeats
Abstract

Aim: To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves., Methods: DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit., Results: DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles., Conclusions: The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method.

Published
2007

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