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Powerplex y23 kit

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The PowerPlex®Y23 kit is a STR (short tandem repeat) multiplex system designed for human identification purposes. It co-amplifies 23 Y-chromosome-specific loci and includes amelogenin for gender determination. The kit is intended for forensic and paternity testing applications.

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Lab products found in correlation

Powerplex esi kit, by Promega (2 mentions) Applied biosystems geneamp pcr system 9700, by Thermo Fisher Scientific (2 mentions) Abi prism 310 genetic analyzer, by Thermo Fisher Scientific (2 mentions) Ab 7300 real time pcr system, by Thermo Fisher Scientific (1 mentions) Quantifiler human dna quantification kit, by Thermo Fisher Scientific (1 mentions)

6 protocols using powerplex y23 kit

1

Updated Y-STR Nomenclature Protocol

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The nomenclature of the RM Y-STRs was updated to comply with the guidelines of the International Society of Forensic Genetics—ISFG [Gusmão et al., 2006 (link)], and to incorporate new variation observed in repeat structures. As such, all data collated were translated to comply with the updated nomenclature. Supp. Table S3 shows the repeat structure and allele designations used during the project, determined in collaboration with Life Technologies and L. Gusmao (IPATIMUP, Porto, Portugal). The RM Y-STR nomenclature used in the present study is in agreement with that used in the Powerplex® Y23 kit (Promega, Madison, WI) and in the Yfiler Plus Y-STR kit (Life Technologies) for the RM Y-STR markers included, respectively.
Ballantyne K.N., Ralf A., Aboukhalid R., Achakzai N.M., Anjos M.J., Ayub Q., Balažic J., Ballantyne J., Ballard D.J., Berger B., Bobillo C., Bouabdellah M., Burri H., Capal T., Caratti S., Cárdenas J., Cartault F., Carvalho E.F., Carvalho M., Cheng B., Coble M.D., Comas D., Corach D., D'Amato M.E., Davison S., de Knijff P., De Ungria M.C., Decorte R., Dobosz T., Dupuy B.M., Elmrghni S., Gliwiński M., Gomes S.C., Grol L., Haas C., Hanson E., Henke J., Henke L., Herrera-Rodríguez F., Hill C.R., Holmlund G., Honda K., Immel U.D., Inokuchi S., Jobling M.A., Kaddura M., Kim J.S., Kim S.H., Kim W., King T.E., Klausriegler E., Kling D., Kovačević L., Kovatsi L., Krajewski P., Kravchenko S., Larmuseau M.H., Lee E.Y., Lessig R., Livshits L.A., Marjanović D., Minarik M., Mizuno N., Moreira H., Morling N., Mukherjee M., Munier P., Nagaraju J., Neuhuber F., Nie S., Nilasitsataporn P., Nishi T., Oh H.H., Olofsson J., Onofri V., Palo J.U., Pamjav H., Parson W., Petlach M., Phillips C., Ploski R., Prasad S.P., Primorac D., Purnomo G.A., Purps J., Rangel-Villalobos H., Rębała K., Rerkamnuaychoke B., Gonzalez D.R., Robino C., Roewer L., Rosa A., Sajantila A., Sala A., Salvador J.M., Sanz P., Schmitt C., Sharma A.K., Silva D.A., Shin K.J., Sijen T., Sirker M., Siváková D., Škaro V., Solano-Matamoros C., Souto L., Stenzl V., Sudoyo H., Syndercombe-Court D., Tagliabracci A., Taylor D., Tillmar A., Tsybovsky I.S., Tyler-Smith C., van der Gaag K.J., Vanek D., Völgyi A., Ward D., Willemse P., Yap E.P., Yong R.Y., Pajnič I.Z, & Kayser M. (2014). Toward Male Individualization with Rapidly Mutating Y-Chromosomal Short Tandem Repeats. Human Mutation, 35(8), 1021-1032.
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2

DNA Profiling of Buccal Swab Samples

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Referent samples (12 buccal swabs) from potential living relatives were collected, recorded, and preliminarily labeled by local DNA experts. Living relatives were directly contacted by a local person (Mr Jure Lauc), who was present during the collection of each sample. Collection was performed with an Internal GENOS collection kit, and dried and labeled samples were transported to the laboratory. Upon arrival, the samples were relabeled and the relevant information entered into the Chain of Custody forms. The samples were stored at -80°C until DNA extraction was performed using the QIAmp DNA Mini Kit (14 ).
PowerPlex® ESI kit (Promega Corp.) was used for further analysis. Similar amounts of DNA were used in all PCR reactions. Amplification was carried out as described previously (12 ). The total reaction volume was 10 μL. Additionally, PowerPlex®Y23 kit (Promega Corp.) was used to simultaneously amplify 23 Y-STR loci according to manufacturer’s recommendations (13 ). PCR amplification was carried out by the Applied Biosystems® GeneAmp® PCR System 9700 (Life Technologies) according to manufacturer’s recommendations. Electrophoresis of the amplification products was performed on an ABI PRISM 310 Genetic Analyzer (Applied Biosystems). The raw data were compiled and analyzed using 310 Data Collection Software and GeneMapperTM 3.2.
Marjanović D., Hadžić Metjahić N., Čakar J., Džehverović M., Dogan S., Ferić E., Džijan S., Škaro V., Projić P., Madžar T., Rod E, & Primorac D. (2015). Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina. Croatian Medical Journal, 56(3), 257-262.
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3

Identifying Carriers of Duplication in PAR1

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One sperm donor (man 20) was previously identified as carrying a duplication of the X chromosome that encompassed the canonical PAR1 boundary and extended at least 12 kb proximal to this (S1 Fig). Twenty-three Y-STRs were typed in 81 donors, including man 20, using the PowerPlex Y23 kit (Promega). Y-chromosome haplogroups were predicted from the resulting STR haplotypes using a Bayesian Allele Frequency approach (http://www.nevgen.org/). Man 20 and man 53 were predicted to carry the haplogroup I2a-L233 sublineage. Two further unrelated ePAR carriers were found by surveying PowerPlex Y23 data to predict haplogroup I2a Y chromosomes among laboratory collections of DNA samples. A first-generation male from CEPH family 1334 (NA12146) was identified as another candidate carrier; he was reported to have an apparent duplication of X-linked SNPs in the vicinity of the ePAR1 (hg19 chrX:2694151–2808548; hg38 chrX:2776110–2890507) in DGV (http://dgv.tcag.ca/dgv/app/home), and predicted to belong to the same I2a sub-haplogroup based on his Y-STR profile (data kindly provided by C.Tyler-Smith, Wellcome Trust Sanger Institute). We also typed two Hungarian males known from sequencing of 3.4Mb of their male specific Y to have the most distantly related I2a sublineage (I2a-M423) [66 (link)] to determine whether all males within I2a possessed an ePAR.
Poriswanish N., Neumann R., Wetton J.H., Wagstaff J., Larmuseau M.H., Jobling M.A, & May C.A. (2018). Recombination hotspots in an extended human pseudoautosomal domain predicted from double-strand break maps and characterized by sperm-based crossover analysis. PLoS Genetics, 14(10), e1007680.
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4

STR Profiling of DNA Samples

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The DNA concentration was determined using Quantifiler Human DNA Quantification Kit (Applied Biosystems Foster City, CA, USA) (11 ). The reaction was carried out in the AB 7300 Real-Time PCR System (Applied Biosystems) according to manufacturer’s recommendations.
The PowerPlex®ESI kit (Promega Corp., Madison, WI, USA) was used to simultaneously amplify 15 STR loci: D3S1358, D8S1179, D18S51, D21S11, FGA, TH01, vWA, D2S441, D10S1248, D22S1045, D1S1656, D12S391, D2S1338, D16S539, D19S433 as well as the gender determination locus, Amelogenin. Amplification was carried out as described previously (12 ). The total volume of each reaction was 25 μL. Additionally, the PowerPlex®Y23 kit (Promega Corp.) was used to simultaneously amplify 23 Y-STR loci according to manufacturer’s recommendations (13 ). PCR amplification was carried out using the Applied Biosystems® GeneAmp® PCR System 9700 (Life Technologies) according to manufacturer’s recommendations. Electrophoresis of the amplification products was performed on an ABI PRISM 310 Genetic Analyzer (Applied Biosystems). The raw data were compiled and analyzed using 310 Data Collection Software and GeneMapperTM 3.2.
Marjanović D., Hadžić Metjahić N., Čakar J., Džehverović M., Dogan S., Ferić E., Džijan S., Škaro V., Projić P., Madžar T., Rod E, & Primorac D. (2015). Identification of human remains from the Second World War mass graves uncovered in Bosnia and Herzegovina. Croatian Medical Journal, 56(3), 257-262.
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5

Optimized PowerPlex Y23 Amplification

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We optimized the amplification protocol of the PowerPlex ® Y23 kit (Promega) based on the manufacturer's recommendations. Reactions with 25, 26, and 27 thermal cycles were performed for one and two 1.2 mm-diameter discs, which we named samples 1 and 2, for each cycle. Two different concentrations of the mix with reduced volume were used: 1.6 µL PowerPlex ® Y23 5X master mix (equivalent to 32% of the recommended amount), 0.8 µL PowerPlex ® Y23 10X primer pair mix (equivalent to 32% of the recommended amount), and 5.6 µL ultra-pure water (equivalent to 32% of the recommended amount); 1.0 µL PowerPlex ® Y23 5X master mix (equivalent to 20% of recommended amount); 0.5 µL PowerPlex ® Y23 10X primer pair mix (equivalent to 20% of the recommended amount), and 3.5 µL ultra-pure water -3.5 (equivalent to 20% of the recommended amount). Eppendorf Research ® 0.5-10 mL, 10-100 mL and 100-1,000 mL micropipettes were used to dispense liquids manually, and thermocycling was performed in a Veriti thermal cycler's 96-well format (Applied Biosystems). In addition, controls with 100% reaction volume were used along with the samples.
Souza C.A., Oliveira T.C., Crovella S., Santos S.M., Rabêlo K.C.N., Soriano E.P., Carvalho M.V.D., Junior A.F.C., Porto G.G., Campello R.I.C., Antunes A.A., Queiroz R.A, & Souza S.M. (2017). Validation of a reaction volume reduction protocol for analysis of Y chromosome haplotypes targeting DNA databases. Genetics and molecular research : GMR, 16(2).
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6

Y-STR Profiling Using ABI 3500

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The ABI 3500 8-capillary genetic analyzer (Applied Biosystems) was used with the POP-4 TM polymer (Performance Optimized Polymer) (Applied Biosystems). Injection parameters specified by the PowerPlex ® Y23 kit (Promega) were used.
The Y chromosome STR fragments were analyzed using the GeneMapper ID-X v 1.2.1 software (Applied Biosystems, 2009) after importing the PowerPlex ® Y23 panels, bins, and stutter text files. The previously validated value of 100 rfus (Relative Fluorescence Units) was used as the peak height analysis threshold.
Souza C.A., Oliveira T.C., Crovella S., Santos S.M., Rabêlo K.C.N., Soriano E.P., Carvalho M.V.D., Junior A.F.C., Porto G.G., Campello R.I.C., Antunes A.A., Queiroz R.A, & Souza S.M. (2017). Validation of a reaction volume reduction protocol for analysis of Y chromosome haplotypes targeting DNA databases. Genetics and molecular research : GMR, 16(2).
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