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Genescan v 3

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Genescan v. 3.7 is a software application for DNA fragment analysis developed by Thermo Fisher Scientific. It provides automated data collection, analysis, and interpretation of results from DNA sequencing experiments.

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Lab products found in correlation

Ampflstr yfiler, by Thermo Fisher Scientific (2 mentions)

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Genescan 3.7 software

3 protocols using genescan v 3

1

Analyzing Y-Chromosome Diversity through SNPs and Microsatellites

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Twenty one SNPs were analyzed through three different techniques (Table S2): RFLP (Bailliet et al. 2009 ) (Table S3), APLP (Jurado Medina et al. 2014) of 400 to 800 bp fragments with known flanking and previously described SNPs (Battaglia et al. 2013 , Y Chromosome Consortium 2002 , Karafet et al. 2008 , Shen et al. 2004 , Underhill et al. 2001 ) (https://www.familytreedna.com/groups/y-dna-q) (Table S4). Due to sequencing difficulties, we replaced Z780 by CTS2730A since both determine the same phylogenetic status.
We analyzed 17 microsatellites (AmpFLSTR® Yfiler® Life Technologies) using Genescan v. 3.7 (Applied Biosystems). Electrophoresis was performed in an ABBI 3130 analyzer. Our Laboratory has been granted the YHRD Quality Test Certificate for Yfiler analysis.
We built median-joining networks (Bandelt, Forster & Röhl 1999) using the NETWORK software (fluxus-engineering.com) with weights assigned following Muzzio et al. (2010) . We used Rho dating methods (Forster et al. 1996 , Saillard et al. 2000) , considering the rate based on population comparison 6.9 104/ STR/generation (Zhivotovsky et al. 2004 ). The geographic distribution of different sub-haplogroups was analyzed by building isofrequency graphs with Surfer12 software, applying the Kriging algorithm each time that the number of samples was higher than 20 (Golden Software 2002) .
Jurado Medina L.S., Paz Sepúlveda P.B., Ramallo V., Sala C., Beltramo J., Schwab M., Motti J.M.B., Santos M.R., Cuello M.V., Salceda S., Dipierri J.E., Alfaro Gómez E.L., Muzzio M., Bravi C.M, & Bailliet G. (2021). Continental Origin for Q Haplogroup Patrilineages in Argentina and Paraguay. Human biology, 92(2).
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2

C9orf72 Repeat Expansion Screening

Cited 2 times
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Most of the patients (n = 94) were initially checked for C9orf72 hexanucleotide repeat expansions at the Neurogenetics Laboratory of Eginition Hospital according to a two-step protocol. This protocol included sizing PCR (amplification of the region that contains the hexanucleotide repeat with primers flanking this region), agarose electrophoresis and fragment analysis to identify samples with possible presence of the C9orf72 repeat expansion. This was followed by repeat primed PCR, to verify and separate samples with the C9orf72 repeat expansion, as previously described [21 (link),22 (link)]. Samples were then electrophorized on an ABI 310 Capillary Analyzer (Applied Biosystems, Foster City, CA, USA) and analyzed on GeneScan v3.7 (2001, Applied Biosystems, Foster City, CA, USA). In addition, 21 patients were initially analyzed for the presence of C9orf72 repeat expansion by repeat primed PCR amplification and STR (short tandem repeats) PCR analysis at the Diagnostic Service Facility, Laboratory of Neurogenetics, University of Antwerp, Belgium.
Bourbouli M., Paraskevas G.P., Rentzos M., Mathioudakis L., Zouvelou V., Bougea A., Tychalas A., Kimiskidis V.K., Constantinides V., Zafeiris S., Tzagournissakis M., Papadimas G., Karadima G., Koutsis G., Kroupis C., Kartanou C., Kapaki E, & Zaganas I. (2021). Genotyping and Plasma/Cerebrospinal Fluid Profiling of a Cohort of Frontotemporal Dementia–Amyotrophic Lateral Sclerosis Patients. Brain Sciences, 11(9), 1239.
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3

Analyzing Y-Chromosome Diversity through SNPs and Microsatellites

Check if the same lab product or an alternative is used in the 5 most similar protocols
Twenty one SNPs were analyzed through three different techniques (Table S2): RFLP (Bailliet et al. 2009 ) (Table S3), APLP (Jurado Medina et al. 2014) of 400 to 800 bp fragments with known flanking and previously described SNPs (Battaglia et al. 2013 , Y Chromosome Consortium 2002 , Karafet et al. 2008 , Shen et al. 2004 , Underhill et al. 2001 ) (https://www.familytreedna.com/groups/y-dna-q) (Table S4). Due to sequencing difficulties, we replaced Z780 by CTS2730A since both determine the same phylogenetic status.
We analyzed 17 microsatellites (AmpFLSTR® Yfiler® Life Technologies) using Genescan v. 3.7 (Applied Biosystems). Electrophoresis was performed in an ABBI 3130 analyzer. Our Laboratory has been granted the YHRD Quality Test Certificate for Yfiler analysis.
We built median-joining networks (Bandelt, Forster & Röhl 1999) using the NETWORK software (fluxus-engineering.com) with weights assigned following Muzzio et al. (2010) . We used Rho dating methods (Forster et al. 1996 , Saillard et al. 2000) , considering the rate based on population comparison 6.9 104/ STR/generation (Zhivotovsky et al. 2004 ). The geographic distribution of different sub-haplogroups was analyzed by building isofrequency graphs with Surfer12 software, applying the Kriging algorithm each time that the number of samples was higher than 20 (Golden Software 2002) .
Medina J., Sepúlveda P.B.P., Ramallo V., Sala C.C., Beltramo J., Schwab M., Motti J.M.B., Santos M.R., Cuello M., Salceda S.A., Dipierri J.E., Gómez E.L.A., Muzzio M., Bravi C.M., & Bailliet G. (2020). Continental Origin for Q Haplogroup Patrilineages in Argentina and Paraguay. Human Biology.
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