Genemapper id x software version 1

Manufactured by Thermo Fisher Scientific

Sourced in United States

GeneMapper ID-X Software Version 1.4 is a data analysis software for capillary electrophoresis-based genetic analysis. It provides tools for analyzing DNA fragment data generated from genetic analysis instruments.

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GeneMapper software (389 citations) GeneMapper (100 citations) GeneMapper ID-X software (28 citations) GeneMapper ID software (22 citations) GeneMapper ID-X (12 citations) GeneMapper® ID-X 1.3 software (9 citations) GeneMapper ID-X version 1.5 Software (4 citations)

12 protocols using genemapper id x software version 1

Precise Allele Determination via Capillary Electrophoresis

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The PCR products were size separated with the help of capillary electrophoresis using an ABI 3100 Genetic Analyzer (Life Technologies Corporation, USA) and size-characterized with the GeneScan 500 LIZ internal lane size standard (Thermo Fisher Scientific) as per the manufacturer’s recommended protocol. The GeneMapper ID-X Software Version 1.4 (Applied Biosystems) was used to determine the amplified fragments’ sizes. All alleles’ designations were based on a comparison with the allelic ladders provided by the AmpFLSTR Yfiler™ system (Thermo Fisher Scientific). The present study was carried out in accordance with the quality assurance standards recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM) [16 ].

Mishra A., Gondhali U., Mishra S, & Choudhary S.K. (2021). Assessment of Genetic Polymorphisms in the Rewa Population of Central India Using Y-Chromosomal STR Markers. Modern Technologies in Medicine, 13(6), 43-55.

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STR Profiling of Cell Lines

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The DNAs from KKU‐055‐CSC and parental KKU‐055 cells were extracted using the genomic extraction kit (Qiagen). A standard STR profile was obtained with 15 loci and the gender marker (amelogenin), amplified using the AmplFLSTR PCR Amplification kit and analyzed by 3130xl Genetic Analyzer (Applied Biosystems). Obtained data were analyzed using the GeneMapper ID‐X Software version 1.4 (Applied Biosystems).

Panawan O., Silsirivanit A., Chang C., Putthisen S., Boonnate P., Yokota T., Nishisyama‐Ikeda Y., Detarya M., Sawanyawisuth K., Kaewkong W., Muisuk K., Luang S., Vaeteewoottacharn K., Kariya R., Yano H., Komohara Y., Ohta K., Okada S., Wongkham S, & Araki N. (2023). Establishment and characterization of a novel cancer stem‐like cell of cholangiocarcinoma. Cancer Science, 114(8), 3230-3246.

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Multiplex Genotyping of Forensic Markers

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Twenty-three autosomal markers (D3S1358, vWA, D16S539, CSF1PO, D6S1043, D8S1179, D21S11, D18S51, D5S818, D2S441, D19S433, FGA, D10S1248, D22S1045, D1S1656, D13S317, D7S820, Penta E, Penta D, TH01, D12S391, D2S1338, and TPOX), a quality indicator system, and amelogenin (AMEL), sex-identification markers were amplified using the commercial VeriFiler Plus PCR Amplification Kit, according to the manufacturer’s protocol. The amplicons were genotyped by multi-capillary electrophoresis on an Applied Biosystems 3130xl Genetic Analyzer, and the allele calling was performed by the GeneMapper ID-X Software Version 1.4 (Applied Biosystems).

Nukpook T., Ekalaksananan T., Kiyono T., Kasemsiri P., Teeramatwanich W., Vatanasapt P., Chaiwiriyakul S., Ungarreevittaya P., Kampan J., Muisuk K, & Pientong C. (2021). Establishment and genetic characterization of cell lines derived from proliferating nasal polyps and sinonasal inverted papillomas. Scientific Reports, 11, 17100.

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Forensic Identification via DNA Profiling

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Further, visualization and identification of reaction products were performed by capillary electrophoresis and automatic LASER fluorescent detection using the ABI 3500 genetic analyzer (Applied Biosystems, Waltham, MA, USA). Data analysis was conducted using Gene Mapper ID-X Software version 1.4 (Applied Biosystems, Waltham, MA, USA). DNA profiles obtained from the bones and teeth of our unidentified subjects were analyzed and compared to those obtained from living relatives. DNA genotypes from living relatives were obtained by analyzing the DNA isolated from saliva.
Data interpretation was carried out with the help of the GenoProof 3-Parentage Examination software, version 3.0.4 (Qualitype, Dresden, Germany) according to the recommendations of the Paternity Testing Commission of the International Society of Forensic Genetics.

Stan E., Muresan C.O., Dumache R., Ciocan V., Ungureanu S., Mihailescu A., Daescu E., Duda-Seiman C., Menghiu G., Hutanu D, & Enache A. (2024). From Jane Doe to Sofia: DNA Extraction Protocol from Bones and Teeth without Liquid Nitrogen for Identifying Skeletal Remains. International Journal of Molecular Sciences, 25(10), 5114.

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Forensic STR Genotyping Protocol

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The samples were genotyped using the PowerPlex^® Fusion 6C System (Promega). DNA amplification was carried out using the GeneAmp^® PCR System 9700 (Applied Biosystems) or the ProFlex™ 3×32-Well PCR System (Applied Biosystems). The PCR products were detected using an ABI 3500 or 3500xL Genetic Analyzer (Thermo Fisher Scientific) equipped with a 36 cm capillary array and POP4^® polymer from Applied Biosystems. Initial fragment sizing and allele calling were performed using GeneMapper^® ID-X software version 1.4 (Applied Biosystems) with a 50 RFU analytical threshold. STR loci with heterozygote balance (Hb) < 0.7 were considered imbalanced.

Worrapitirungsi W., Sathirapatya T., Sukawutthiya P., Vongpaisarnsin K, & Varrathyarom P. (2024). Assessing the feasibility of free DNA for disaster victim identification and forensic applications. Scientific Reports, 14, 5411.

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Autosomal STR Marker Analysis

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Samples were analyzed on a 3500 Genetic Analyzer following the manufacturer's recommendations. As autosomal STR markers, we used 1µL of the amplified PCR product (DNA sample) and 1µL of the Allelic Ladder (AL). They were added into the mix containing 12.5µL of Hi-Di Formamide (Applied Biosystems, USA) and 0.5µL DNA size standard BTO (Qiagen, Germany). Gene Mapper ID-X Software version 1.4 (Applied Biosystems, USA) was used to analyze the obtained data. For the statistical calculation, we used the Genoproof-3 Chimerism testing (Qualitype, Germany).

Dumache R., Lascu A., Ciocan V., Mureșan M.C., Mihăilescu A., Enache A., & Arghirescu S. (2021). Allogeneic Hematopoietic Stem Cell Transplantation in Fanconi Anemia. Annals of Hematology & Oncology, 8(9).

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DNA STR Marker Profiling Protocol

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For fragment separation, a mixture of 2–5 µl amplified PCR product, 23.5 µl HiDiTM formamide (Thermo Fisher Scientific Corporation) and 1.5 µl GeneScanTM 600 LIZ ® dye Size Standard v2.0 (Thermo Fisher Scientific Corporation) was injected in an ABI 3500 Genetic Analyzer (Thermo Fisher Scientific Corporation). The obtained DNA STR marker profiles were then analysed, and profile quality was evaluated (GeneMapper ® ID-X software Version 1.4, Thermo Fisher Scientific Corporation). Here, the minimum signal strength analysed was 50 relative fluorescent units (RFU). Profile completeness was calculated as the percentage of observed alleles out of a full STR marker profile. A full profile is represented by 68 alleles in total: 17 STR marker systems with two heterozygous or homozygous single alleles per system in two PCR approaches. Average success rates per tissue type were then accessorily calculated.

Helm K., Matzenauer C., Neuhuber F., Monticelli F., Meyer H., Pittner S, & Gotsmy W. (2021). Suitability of specific soft tissue swabs for the forensic identification of highly decomposed bodies. International Journal of Legal Medicine, 135(4), 1319-1327.

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Genotyping of Kuwaiti Individuals

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Blood samples were collected on Whatman FTA cards (GE Healthcare Life Sciences, IL, USA) from 400 unrelated Kuwaiti (253 males and 147 females). DNA was amplified directly, without quantification, from a 1.2 mm FTA card punch, according to the directions in the PowerPlex Fusion 6C manual, using a SureCycler 8800 thermal cycler (Agilent Technologies, CA, USA). Detection and separation of the DNA fragments were carried out using an Applied Biosystems 3500 Genetic Analyzer (Thermo Fisher Scientific) with the internal lane standard WEN ILS 500 and allelic ladder provided with the PowerPlex Fusion 6C kit. Genotype determination and allele calling for only the 23 autosomal loci were carried out using GeneMapper ID-X software version 1.4 (Thermo Fisher Scientific).

Haidar M., Abbas F.A., Alsaleh H, & Haddrill P.R. (2021). Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population. Scientific Reports, 11, 1865.

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Genetic Profiling Using STR Kits

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DNA extracts were amplified using the AmpFLSTR™ NGM SElect™ [47] (link) and the NGM Detect™ [48] (link) PCR amplification kits (both from Thermo Fisher Scientific), according to the manufacturers' instructions. 30 amplification cycles were run with both STR kits. Amplicons of the STR loci were up to 450 bp (NGM SElect) and 380 bp (NGM Detect) in length. Genetic sex of the individuals was determined by amelogenin analysis, included in the NGM SElect and NGM Detect kits.
For Y-STR analysis, DNA extracts were amplified using the Power-Plex® Y23 System (Promega) [49] (link) and the Yfiler™ Plus (Thermo Fisher Scientific) [50] (link) PCR amplification kits, according to the manufacturers' instructions. PowerPlex Y23 amplicons were up to 425 bp in length, the Yfiler Plus amplicons were up to 478 bp in length.
PCR products were separated and detected with a Genetic Analyzer 3130xl or a Genetic Analyzer 3500. In general, a peak detection threshold of 50 rfu was used for declaring positive results. Exceptionally, lower peaks were called manually. Raw data were analyzed with the Genemapper ID-X Software Version 1.4 (Thermo Fisher Scientific).

Alterauge A., Lösch S., Sulzer A., Gysi M, & Haas C. (2021). Beyond simple kinship and identification: aDNA analyses from a 17th-19th century crypt in Germany. Forensic science international. Genetics, 53.

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Ultra-low DNA Quantification Protocol

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EPGs of single-source DNA samples were obtained for DNA quantities of 10 pg, 7.5 pg, 5 pg, 2.5 pg, 1 pg, 0.75 pg, 0.5 pg and 0.25 pg. This range was chosen because it created EPGs ranging from having no allele or locus drop-outs to showing all loci dropping out.¹Two kits were used for the DNA amplification: AmpFlSTR Identifiler Plus (29 cycles) and PowerPlex 16 HS by Promega (32 cycles). Capillary electrophoresis separated and detected the PCR products on am ABI 3130xl genetic sequencer. GeneMapper ID-X software version 1.3 by Applied Biosystems was used for analyzing the DNA typing results. For further details on the analytical procedure, we refer the reader to [11 ].

Gittelson S., Steffen C.R, & Coble M.D. (2016). Low-template DNA: A single DNA analysis or two replicates?. Forensic science international, 264, 139-145.

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