Turkiye Klinikleri Journal of Forensic Medicine and Forensic Sciences

.: ORIGINAL RESEARCH
Determination of Gene Frequency of 10 New STR Loci in Turkey: Experimental Research
Yeni 10 STR Lokusunun Türkiye'deki Gen Sıklığının Belirlenmesi: Deneysel Çalışma
Tuğba SOHTORİK ÖZTÜRKa, Özlem BÜLBÜLa, Gönül FİLOĞLU TÜFEKa
aDepartment of Biology, İstanbul University-Cerrahpaşa Institute of Forensic Medicine and Forensic Sciences, İstanbul, Türkiye
Turkiye Klinikleri J Foren Sci Leg Med. 2022;19(3):149-57
doi: 10.5336/forensic.2022-89168
Article Language: EN
Full Text
ABSTRACT
 Objective: Short tandem repeats (STRs) have been widely used in human identification in forensics. Evaluation and design of new markers are useful tools to obtain additional information and complete conventional analysis. Also, it will be an alternative way to confirm the results in the problematic cases (complex kinship, degraded samples, etc.). Increasing the number of loci will result in reducing the risk of adventitious matches in countries that have a national DNA database. In this study, we investigated allele frequencies of the 10 non-Combined DNA Index System STR loci (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D21S2055, D10S2325) by using Investigator® HDplex kit. Material and Methods: DNAs were extracted from 100 blood samples by using the QIAmp DNA Mini Kit (Qiagen). STR loci were amplified according to Investigator® HDplex kit. Polymerase chain reaction products were separated with ABI 3130 Genetic Analyzer and analyzed with GeneMapper IDX software. Forensic and population parameters were estimated with the Promega PowerStats Excel sheet. Allele frequencies, p-values for Hardy-Weinberg equilibrium, and population differentiation based on the loci (Fst) were calculated with Arlequin ver.3.5. Results: We observed that all STR loci showed high power of discrimination. For population comparison, we found statistically significant differences between Türkiye and African, East Asian, and American populations at a couple of STR loci. Besides, there was no statistically significant variation between Turkish and European populations as expected. Conclusion: This study provides Turkish population data for forensic laboratories and this kit can be used to support the existing STR loci.

Keywords: Non-CODIS; DNA analysis; new short tandem repeat loci
ÖZET
 Amaç: Otozomal kısa ardışık tekrar [short tandem repeat (STR)] lokusları, adli vakalarda kişi identifikasyonunda yaygın olarak kullanılmaktadır. Yeni belirteçlerin araştırılması ve dizayn edilmesi geleneksel analizleri tamamlayıcı olduğu gibi kardeşlik ve akrabalık ilişkilerinin söz konusu olduğu kompleks vakalarda ya da zorlukların yaşanabildiği bazı durumlarda (degrade örnekler vs.) sonuçların alternatif yollarla teyit edilmesini mümkün kılmaktadır. Araştırılan lokus sayısının artırılması veritabanı uygulaması olan ülkelerde yanlış eşleşme riskini de azaltmaktadır. Bu çalışmada, 'Combined DNA Index System'de yer almayan, yaygın olarak kullanılan STR lokuslarından farklı, 10 yeni STR lokusunun (D7S1517, D3S1744, D12S391, D2S1360, D6S474, D4S2366, D8S1132, D5S2500, D21S2055, D10S2325) Türkiye'deki gen sıklığı Investigator® HDplex kiti kullanılarak incelendi. Gereç ve Yöntemler: DNA analizi için 100 g.nüllüden kan örneği alındı ve DNA izolasyonu QIAmp DNA Mini Kit (Qiagen) protokolüne uygun olarak gerçekleştirildi. STR lokusları Investigator® HDplex Kit protokolüne uygun olarak çoğaltıldı. Polimeraz zincir reaksiyonu ürünleri ABI 3130 Genetik Analizörde yürütüldü ve GeneMapper IDX ile analiz edildi. Popülasyon ve adli istatistik parametreleri Promega Power-Stats Excel kullanılarak hesaplandı. Alel frekansları, Hardy-Weinberg dengesi ve popülasyonlar arası lokus bazındaki farklılıklar (Fst) Arlequin v.3.5 programı kullanılarak hesaplandı. Bulgular: Tüm STR lokuslarının yüksek ayrım gücüne sahip olduğu gözlendi. Türkiye ile Afrika, Doğu Asya ve Amerika popülasyonları arasında bir kaç lokusta istatistiksel olarak anlamlı farklılıklar bulunurken; Avrupa popülasyonu ile istatistiksel olarak anlamlı bir farklılık gözlenmedi. Sonuç: Bu çalışma adli laboratuvarlar için Türk popülasyonu verileri sağlamaktadır ve çalışma bulgularına göre söz konusu kitin adli laboratuvarlarda mevcut STR lokuslarını desteklemek amacıyla güvenilirlikle kullanılabileceği gösterilmiştir.

Anahtar Kelimeler: Non-CODIS; DNA analizi; yeni kısa ardışık tekrar lokusları
REFERENCES:
  1. Butler JM. Forensic DNA Typing: Biology, Technology and Genetics of STR Markers. 2nd ed. USA: Elsevier Academic Press; 2005.
  2. Robertson J, Ross AM, Burgayne LA. DNA in Forensic Science: Theory, Techniques and Applications. 3rd ed. Longooddon: Ellis Howard Ltd; 1990. [Crossref] 
  3. Jeffreys AJ, Wilson V, Thein SL. Hypervariable 'minisatellite' regions in human DNA. Nature. 1985;314(6006):67-73. [Crossref]  [PubMed] 
  4. Reno J, Marcus D, Leary ML, Samuels JE. The future of Forensic DNA Testing: Predictions of the Research and Development Working Group. National Institutes of Justice, National Commision on the Future of DNA Evidence; 2000. Report no.: NCJ 18397. [Link] 
  5. Filoglu G, Altuncul H, Bulbul O. Adli Genetik ve Genetik Kimliklendirme. 1. Baskı. Ankara: Seçkin Yayınevi; 2021.
  6. Butler JM, Hill CR, Decker AE, Kline MC, Vallone PM. New autosomal STR loci. Forensic Science International: Genetics Supplement Series. 2008;1:95-6. [Crossref] 
  7. Qiagen [Internet]. © QIAGEN 2013-22. All rights reserved [Cited: April 5, 2022]. Population data for Investigator HDplex - (EN). Available from: [Link] 
  8. Phillips C, Fernandez-Formoso L, Gelabert-Besada M, García-Magari-os M, Amigo J, Carracedo A, et al. Global population variability in Qiagen Investigator HDplex STRs. Forensic Sci Int Genet. 2014;8(1):36-43. [Crossref]  [PubMed] 
  9. Gettings KB, Borsuk LA, Steffen CR, Kiesler KM, Vallone PM. Sequence-based U.S. population data for 27 autosomal STR loci. Forensic Sci Int Genet. 2018;37:106-15. [Crossref]  [PubMed]  [PMC] 
  10. Hares DR. Selection and implementation of expanded CODIS core loci in the United States. Forensic Sci Int Genet. 2015;17:33-4. [Crossref]  [PubMed] 
  11. Gettings KB, Kiesler KM, Faith SA, Montano E, Baker CH, Young BA, et al. Sequence variation of 22 autosomal STR loci detected by next generation sequencing. Forensic Sci Int Genet. 2016;21:15-21. [Crossref]  [PubMed]  [PMC] 
  12. AmpFlSTR® Identifiler® Plus PCR Amplification Kit User Guide, Applied BiosystemsTM. 2015. Cited: April 5, 2022. Available from: [Link] 
  13. ForenSeq? DNA Signature Prep Reference Guide, Verogen. 2018. Cited: April 5, 2022. Available from: [Link] 
  14. GlobalFilerTM PCR Amplification Kit User Guide, Applied BiosystemsTM, 4476135(4477604). 2016. p.1-166. Cited: April 5, 2022. Available from: [Link] 
  15. Qiagen [Internet]. © QIAGEN 2013-22. All rights reserved [Cited: April 5, 2022]. Investigator® ESSplex SE QS Kit Handbook. Available from: [Link] 
  16. Qiagen [Internet]. © QIAGEN 2013-22. All rights reserved [Cited: April 5, 2022]. Investigator® 24plex QS Handbook (EN). Available from: [Link] 
  17. PowerPlex® 21 System for Use on the Applied Biosystems® Genetic Analyzers. Promega. 2021. Cited: April 5, 2022. Available from: [Link] 
  18. PowerPlex® 16 HS System for Use on the Applied Biosystems® Genetic Analyzers. Promega Corporation. 2016. Cited: April 5, 2022. Available from: [Link] 
  19. PowerPlex® Fusion 6C System for Use on the Applied Biosystems® Genetic Analyzers. Promega Corporation. 2016. Cited: April 5, 2022. Available from: [Link] 
  20. Precision ID GlobalFiler NGS STR Panels. Thermo Fisher Scientific. 2018. Cited: April 5, 2022. Available from: [Link] 
  21. Hochberg Y. A sharper Bonferroni procedure for multiple tests of significance. Biometrika. 1988;75(4):800-902. [Crossref] 
  22. Zintzaras E. Impact of Hardy-Weinberg equilibrium deviation on allele-based risk effect of genetic association studies and meta-analysis. Eur J Epidemiol. 2010;25(8):553-60. [Crossref]  [PubMed] 
  23. Bulbul O, Fernandez-Formoso L, Phillips C, Altuncul H, Filoglu G, Lareu MV, et al. Allele frequencies of the five new European Standard Set (ESS) STRs and 15 established STRs in a Turkish population. Forensic Sci Int Genet. 2014;9:e26. [Crossref]  [PubMed] 
  24. Tavacı İ, Bülbül O, Filoglu G, Altuncul H. X kromozomunda bulunan 15 SNP lokusunun Türkiye populasyonundaki polimorfizmi [Polymorphism of 15 X-chromosome SNPs in the Turkish population]. J Foren Sci Leg Med. 2020;17(3):238-44. [Crossref] 
  25. Duvenci A, Bulbul O, Filoglu G. Evaluation of population data and forensic parameters of Turkish population on 30 autosomal insertion and deletion polymorphisms. Russian Journal of Genetics. 2019;55(2):246-52. [Crossref] 
  26. Tillmar A, Nilsson H, Kling D, Montelius K. Analysis of investigator HDplex markers in Swedish and Somali populations. Forensic Sci. Int. Genet. 2013;7(1):e21-e2. [Crossref]  [PubMed] 
  27. Zieger M, Gouy A, Utz S. Expanding the Swiss autosomal marker set to 32 STRs. Int J Legal Med. 2021;135(6):2309-10. [Crossref]  [PubMed]  [PMC] 
  28. Jung JY, Kim EH, Oh YL, Park HC, Hwang JH, Lim SK. Evaluation of forensic genetic parameters of 12 STR loci in the Korean population using the InvestigatorⓇ HDplex kit. Int J Legal Med. 2017;131(5):1247-9. [Crossref]  [PubMed] 
  29. Turrina S, Ferrian M, Caratti S, De Leo D. Investigator HDplex markers: allele frequencies and mutational events in a North Italian population. Int J Legal Med. 2015;129(4):731-3. [Crossref]  [PubMed] 
  30. Tereba A. Tools for analysis of population statistics. Promega Corporation. Profiles DNA. 1999;2:14-26. [Link] 
  31. Liu Q, Nan H, He X, Wu W, Lu D. Population genetic data of Investigator HDplex markers in Han population from Southern China. Int J Legal Med. 2019;133(1):77-9. [Crossref]  [PubMed] 
  32. Schmid D, Anslinger K, Rolf B. Allele frequencies of the ACTBP2 (=SE33), D18S51, D8S1132, D12S391, D2S1360, D3S1744, D5S2500, D7S1517, D10S2325 and D21S2055 loci in a German population sample. Forensic Sci Int. 2005;151(2-3):303-5. [Crossref]  [PubMed] 

.: Up To Date

.: Process List

Login

 Forgot your password?

 New Registration  

Contact

Ortadoğu Reklam Tanıtım Yayıncılık Turizm Eğitim İnşaat Sanayi ve Ticaret A.Ş.

.: Address

Turkocagi Caddesi No:30 06520 Balgat / ANKARA
Phone: +90 312 286 56 56
Fax: +90 312 220 04 70
E-mail: info@turkiyeklinikleri.com

.: Manuscript Editing Department

Phone: +90 312 286 56 56/ 2
E-mail: yaziisleri@turkiyeklinikleri.com

.: English Language Redaction

Phone: +90 312 286 56 56/ 145
E-mail: tkyayindestek@turkiyeklinikleri.com

.: Marketing Sales-Project Department

Phone: +90 312 286 56 56/ 142
E-mail: reklam@turkiyeklinikleri.com

.: Subscription and Public Relations Department

Phone: +90 312 286 56 56/ 118
E-mail: abone@turkiyeklinikleri.com

.: Customer Services

Phone: +90 312 286 56 56/ 118
E-mail: satisdestek@turkiyeklinikleri.com

1. TERMS OF USE

1.1. To use the web pages with http://www.turkiyeklinikleri.com domain name or the websites reached through the sub domain names attached to the domain name (They will be collectively referred as "SITE"), please read the conditions below. If you do not accept these terms, please cease to use the "SITE." "SITE" owner reserves the right to change the information on the website, forms, contents, the "SITE," "SITE" terms of use anytime they want.

1.2. The owner of the "SITE" is Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc. (From now on it is going to be referred as "Turkiye Klinikleri", shortly) and it resides at Turkocagi cad. No:30, 06520 Balgat Ankara. The services in the "SITE" are provided by "Turkiye Klinikleri."

1.3. Anyone accessing the "SITE" with or without a fee whether they are a natural person or a legal identity is considered to agree these terms of use. In this contract hereby, "Turkiye Klinikleri" may change the stated terms anytime. These changes will be published in the "SITE" periodically and they will be valid when they are published. Any natural person or legal identity benefiting from and reaching to the "SITE" are considered to be agreed to any change on hereby contract terms done by "Turkiye Klinikleri."

1.4. The "Terms of Use" hereby is published in the website with the last change on March 30th 2014 and the "SITE" is activated by enabling the access to everyone. The "Terms of Use" hereby is also a part of the any "USER Contract" was and/or will be done with the users using "Turkiye Klinikleri" services with or without a fee an inseparable.

2. DEFINITIONS

2.1. "SITE": A website offering different kind of services and context with a certain frame determined by "Turkiye Klinikleri" and it is accessible on-line on http://www.turkiyeklinikleri.com domain name and/or subdomains connected to the domain name.

2.2. USER: A natural person or a legal identity accessing to the "SITE" through online settings.

2.3. LINK: A link enabling to access to another website through the "SITE", the files, the context or through another website to the "SITE", the files and the context.

2.4. CONTEXT: Any visual, literary and auditory images published in the "Turkiye Klinikleri", "SITE" and/or any website or any accessible information, file, picture, number/figures, price, etc.

2.5. "USER CONTRACT": An electronically signed contract between a natural or a legal identity benefiting from special services "Turkiye Klinikleri" will provide and "Turkiye Klinikleri".

3. SCOPE OF THE SERVICES

3.1. "Turkiye Klinikleri" is completely free to determine the scope and quality of the services via the "SITE".

3.2. To benefit the services of "Turkiye Klinikleri" "SITE", the "USER" must deliver the features that will be specified by "Turkiye Klinikleri". "Turkiye Klinikleri" may change this necessity any time single-sided.

3.3. Not for a limited number, the services "Turkiye Klinikleri" will provide through the "SITE" for a certain price or for free are;

- Providing scientific articles, books and informative publications for health industry.

- Providing structural, statistical and editorial support to article preparation stage for scientific journals.

4. GENERAL PROVISIONS

4.1. "Turkiye Klinikleri" is completely free to determine which of the services and contents provided in the "SITE" will be charged.

4.2. People benefiting from the services provided by "Turkiye Klinikleri" and using the website can use the "SITE" only according to the law and only for personal reasons. Users have the criminal and civil liability for every process and action they take in the "SITE". Every USER agrees, declares and undertakes that they will not proceed by any function or action infringement of rights of "Turkiye Klinikleri"s and/or other third parties', they are the exclusive right holder on usage, processing, storage, made public and revealing any written, visual or auditory information reported to Turkiye Klinikleri" and/or "SITE" to the third parties. "USER" agrees and undertakes that s/he will not duplicate, copy, distribute, process, the pictures, text, visual and auditory images, video clips, files, databases, catalogs and lists within the "SITE", s/he will not be using these actions or with other ways to compete with "Turkiye Klinikleri", directly or indirectly.

4.3. The services provided and the context published within the "SITE" by third parties is not under the responsibility of "Turkiye Klinikleri", institutions collaborated with "Turkiye Klinikleri", "Turkiye Klinikleri" employee and directors, "Turkiye Klinikleri" authorized salespeople. Commitment to accuracy and legality of the published information, context, visual and auditory images provided by any third party are under the full responsibility of the third party. "Turkiye Klinikleri" does not promise and guarantee the safety, accuracy and legality of the services and context provided by a third party.

4.4. "USER"s cannot act against "Turkiye Klinikleri", other "USER"s and third parties by using the "SITE". "Turkiye Klinikleri" has no direct and/or indirect responsibility for any damage a third party suffered or will suffer regarding "USER"s actions on the "SITE" against the rules of the hereby "Terms of Use" and the law.

4.5. "USER"s accept and undertake that the information and context they provided to the "SITE" are accurate and legal. "Turkiye Klinikleri" is not liable and responsible for promising and guaranteeing the verification of the information and context transmitted to "Turkiye Klinikleri" by the "USER"s, or uploaded, changed and provided through the "SITE" by them and whether these information are safe, accurate and legal.

4.6. "USER"s agree and undertake that they will not perform any action leading to unfair competition, weakening the personal and commercial credit of "Turkiye Klinikleri" and a third party,  encroaching and attacking on personal rights within the "SITE" in accordance with the Turkish Commercial Code Law.

4.7. "Turkiye Klinikleri" reserves the right to change the services and the context within the "SITE"  anytime. "Turkiye Klinikleri" may use this right without any notification and timelessly. "USER"s have to make the changes and/or corrections "Turkiye Klinikleri" required immediately. Any changes and/or corrections that are required by "Turkiye Klinikleri", may be made by "Turkiye Klinikleri" when needed. Any harm, criminal and civil liability resulted or will result from changes and/or corrections required by "Turkiye Klinikleri" and were not made on time by the "USER"s belongs completely to the users.

4.8. "Turkiye Klinikleri" may give links through the "SITE" to other websites and/or "CONTEXT"s and/or folders that are outside of their control and owned and run by third parties. These links are provided for ease of reference only and do not hold qualification for support the respective web SITE or the admin or declaration or guarantee for the information inside. "Turkiye Klinikleri" does not hold any responsibility over the web-sites connected through the links on the "SITE", folders and context, the services or products on the websites provided through these links or their context.

4.9. "Turkiye Klinikleri" may use the information provided to them by the "USERS" through the "SITE" in line with the terms of the "PRIVACY POLICY" and "USER CONTRACT". It may process the information or classify and save them on a database. "Turkiye Klinikleri" may also use the USER's or visitor's identity, address, e-mail address, phone number, IP number, which sections of the "SITE" they visited, domain type, browser type, date and time information to provide statistical evaluation and customized services.

5. PROPRIETARY RIGHTS

5.1. The information accessed through this "SITE" or provided by the users legally and all the elements (including but not limited to design, text, image, html code and other codes) of the "SITE" (all of them will be called as studies tied to "Turkiye Klinikleri"s copyrights) belongs to "Turkiye Klinikleri". Users do not have the right to resell, process, share, distribute, display or give someone permission to access or to use the "Turkiye Klinikleri" services, "Turkiye Klinikleri" information and the products under copyright protection by "Turkiye Klinikleri". Within hereby "Terms of Use" unless explicitly permitted by "Turkiye Klinikleri" nobody can reproduce, process, distribute or produce or prepare any study from those under "Turkiye Klinikleri" copyright protection.

5.2. Within hereby "Terms of Use", "Turkiye Klinikleri" reserves the rights for "Turkiye Klinikleri" services, "Turkiye Klinikleri" information, the products associated with "Turkiye Klinikleri" copyrights, "Turkiye Klinikleri" trademarks, "Turkiye Klinikleri" trade looks or its all rights for other entity and information it has through this website unless it is explicitly authorized by "Turkiye Klinikleri".

6. CHANGES IN THE TERMS OF USE

"Turkiye Klinikleri" in its sole discretion may change the hereby "Terms of Use" anytime announcing within the "SITE". The changed terms of the hereby "Terms of Use" will become valid when they are announced. Hereby "Terms of Use" cannot be changed by unilateral declarations of users.

7. FORCE MAJEURE

"Turkiye Klinikleri" is not responsible for executing late or never of this hereby "Terms of Use", privacy policy and "USER Contract" in any situation legally taken into account as force majeure. Being late or failure of performance or non-defaulting of this and similar cases like this will not be the case from the viewpoint of "Turkiye Klinikleri", and "Turkiye Klinikleri" will not have any damage liability for these situations. "Force majeure" term will be regarded as outside of the concerned party's reasonable control and any situation that "Turkiye Klinikleri" cannot prevent even though it shows due diligence. Also, force majeure situations include but not limited to natural disasters, rebellion, war, strike, communication problems, infrastructure and internet failure, power cut and bad weather conditions.

8. LAW AND AUTHORISATION TO FOLLOW

Turkish Law will be applied in practicing, interpreting the hereby "Terms of Use" and managing the emerging legal relationships within this "Terms of Use" in case of finding element of foreignness, except for the rules of Turkish conflict of laws. Ankara Courts and Enforcement Offices are entitled in any controversy happened or may happen due to hereby contract.

9. CLOSING AND AGREEMENT

Hereby "Terms of Use" come into force when announced in the "SITE" by "Turkiye Klinikleri". The users are regarded to agree to hereby contract terms by using the "SITE". "Turkiye Klinikleri" may change the contract terms and the changes will be come into force by specifying the version number and the date of change on time it is published in the "SITE".

 

30.03.2014

Privacy Policy

We recommend you to read the terms of use below before you visit our website. In case you agree these terms, following our rules will be to your favor. Please read our Terms of Use thoroughly.

www.turkiyeklinikleri.com website belongs to Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc. and is designed in order to inform physicians in the field of health

www.turkiyeklinikleri.com cannot reach to user’s identity, address, service providers or other information. The users may send this information to the website through forms if they would like to. However, www.turkiyeklinikleri.com may collect your hardware and software information. The information consists of your IP address, browser type, operating system, domain name, access time, and related websites. www.turkiyeklinikleri.com cannot sell the provided user information (your name, e-mail address, home and work address, phone number) to the third parties, publish it publicly, or keep it in the website. Gathered information has a directing feature to be a source for the website’s visitor profile, reporting and promotion of the services.

www.turkiyeklinikleri.com uses the taken information:

-To enhance, improve and maintain the quality of the website

-To generate visitor’s profile and statistical data

-To determine the tendency of the visitors on using our website

-To send print publications/correspondences

-To send press releases or notifications through e-mail

-To generate a list for an event or competition

By using www.turkiyeklinikleri.com you are considered to agree that;

-Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc. cannot be hold responsible for any user’s illegal and immoral behavior,

-Terms of use may change from time to time,

-It is not responsible for other websites’ contents it cannot control or the harms they may cause although it uses the connection they provided.

Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc. may block the website to users in the following events:

-Information with wrong, incomplete, deceiving or immoral expressions is recorded to the website,

-Proclamation, advertisement, announcement, libelous expressions are used against natural person or legal identity,

-During various attacks to the website,

-Disruption of the website because of a virus.

Written, visual and audible materials of the website, including the code and the software are under protection by legal legislation.

Without the written consent of Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc. the information on the website cannot be downloaded, changed, reproduced, copied, republished, posted or distributed.

All rights of the software and the design of the website belong to Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc.

Ortadoğu Advertisement Presentation Publishing Tourism Education Architecture Industry and Trade Inc. will be pleased to hear your comments about our terms of use. Please share the subjects you think may enrich our website or if there is any problem regarding our website.

info@turkiyeklinikleri.com