[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-seo-595432-105":3,"detail-sidebar-cat-0-en-105":81,"doc-detail-595432-en":130},{"code":4,"msg":5,"data":6},0,"ok",{"site_id":7,"language":8,"slug":9,"title":10,"keywords":11,"description":12,"schema_data":13,"social_meta":74,"head_meta":76,"extra_data":78,"updated_unix":80},105,"en","alu-insertions-and-genetic-diversity-a-preliminary-investigation-by-an-undergraduate-bioinformatics-class","Alu Insertions and Genetic Diversity - A Preliminary Investigation by an Undergraduate Bioinformatics Class","","Alu-insertion polymorphisms are used by an undergraduate bioinformatics class to investigate how specific insertion sites can inform human population genetics. Allele and genotype Alu frequencies are determined across African-American and Japanese populations with a control group included. The study tests for the presence of Alu insertions on chromosomes 4, 10, and 16 to compare genomic patterns among populations.",{"@graph":14,"@context":73},[15,34,56],{"@type":16,"itemListElement":17},"BreadcrumbList",[18,23,27,31],{"item":19,"name":20,"@type":21,"position":22},"https://docshare.wps.com","Home","ListItem",1,{"item":24,"name":25,"@type":21,"position":26},"https://docshare.wps.com/document/","Document",2,{"item":28,"name":29,"@type":21,"position":30},"https://docshare.wps.com/document/research-report/","Research & Report",3,{"item":32,"name":10,"@type":21,"position":33},"https://docshare.wps.com/document/alu-insertions-and-genetic-diversity-a-preliminary-investigation-by-an-undergraduate-bioinformatics-class/595432/",4,{"url":32,"name":10,"@type":35,"image":36,"author":41,"headline":10,"publisher":44,"fileFormat":47,"inLanguage":8,"description":12,"dateModified":48,"datePublished":49,"encodingFormat":47,"isAccessibleForFree":50,"interactionStatistic":51},"DigitalDocument",{"url":37,"@type":38,"width":39,"height":40},"https://docshare.wps.com/thumbnails/alu-insertions-and-genetic-diversity-a-preliminary-investigation-by-an-undergraduate-bioinformatics-class/595432.png","ImageObject",300,407,{"name":42,"@type":43},"Blitz","Person",{"url":19,"name":45,"@type":46},"DocShare","Organization","application/pdf","2026-10-30","2026-10-15",true,{"@type":52,"interactionType":53,"userInteractionCount":55},"InteractionCounter",{"@type":54},"ViewAction",5,{"@type":57,"mainEntity":58},"FAQPage",[59,65,69],{"name":60,"@type":61,"acceptedAnswer":62},"What genomic markers does the study focus on, and why are they relevant?","Question",{"text":63,"@type":64},"The study focuses on Alu-insertion polymorphisms, a type of short interspersed element (SINE). These insertion sites are considered informative landmarks in human genome evolution and can support population-genetics investigation.","Answer",{"name":66,"@type":61,"acceptedAnswer":67},"Which populations and chromosome locations are compared in the analysis?",{"text":68,"@type":64},"The class compares African-American and Japanese populations against a control group. Presence of Alu insertions is tested on the 4th, 10th, and 16th chromosomes.",{"name":70,"@type":61,"acceptedAnswer":71},"How are DNA samples prepared for downstream PCR amplification?",{"text":72,"@type":64},"Participants collect saliva-saline samples, which are concentrated and processed to obtain a DNA-containing pellet. The DNA is resuspended, treated with Chelex®, heated in a boiling water bath, then clarified by centrifugation before PCR.","https://schema.org",{"og:url":32,"og:type":75,"og:title":10,"og:site_name":45,"og:description":12},"article",{"robots":77,"canonical":32},"index,follow",{"doc_id":79,"site_id":7},595432,1792211335,{"code":4,"msg":82,"data":83},"success",[84,88,92,96,100,105,110,114,119,122,126],{"id":22,"doc_module":4,"doc_module_name":25,"category_name":85,"show_sort_weight":86,"slug":87},"Story & Novel",90,"story-novel",{"id":26,"doc_module":4,"doc_module_name":25,"category_name":89,"show_sort_weight":90,"slug":91},"Literature",80,"literature",{"id":33,"doc_module":4,"doc_module_name":25,"category_name":93,"show_sort_weight":94,"slug":95},"Exam",70,"exam",{"id":55,"doc_module":4,"doc_module_name":25,"category_name":97,"show_sort_weight":98,"slug":99},"Comic",60,"comic",{"id":101,"doc_module":4,"doc_module_name":25,"category_name":102,"show_sort_weight":103,"slug":104},6,"Technology",50,"technology",{"id":106,"doc_module":4,"doc_module_name":25,"category_name":107,"show_sort_weight":108,"slug":109},7,"Healthcare",40,"healthcare",{"id":111,"doc_module":4,"doc_module_name":25,"category_name":29,"show_sort_weight":112,"slug":113},8,30,"research-report",{"id":115,"doc_module":4,"doc_module_name":25,"category_name":116,"show_sort_weight":117,"slug":118},9,"Religion & Spirituality",20,"religion-spirituality",{"id":117,"doc_module":4,"doc_module_name":25,"category_name":120,"show_sort_weight":117,"slug":121},"World Cup","world-cup",{"id":123,"doc_module":4,"doc_module_name":25,"category_name":124,"show_sort_weight":123,"slug":125},10,"Lifestyle","lifestyle",{"id":127,"doc_module":4,"doc_module_name":25,"category_name":128,"show_sort_weight":55,"slug":129},19,"General","general",{"code":4,"msg":82,"data":131},{"doc_id":79,"user_id":132,"nickname":42,"user_avatar":133,"doc_module":4,"category_id":111,"category_name":29,"doc_title":10,"doc_description":12,"doc_content":134,"file_id":135,"file_url":136,"file_type":137,"file_size":138,"view_count":55,"is_deleted":4,"is_public":22,"is_downloadable":22,"audit_status":22,"page_count":101,"language":139,"language_code":8,"site_id":7,"html_lang":8,"table_of_contents":140,"faqs":141,"seo_title":142,"seo_description":12,"update_tm":143,"read_time":144,"preview_page_count":4},24464137899374,"https://us-avatar.wpscdn.com/davatar_3d24733baf745e90a7e4bdd5f77d97b2","Alu Insertions and Genetic Diversity: A Preliminary Investigation by an Undergraduate Bioinformatics Class  \nNancy L. Elwess*, Stephen L. Duprey, Lindesay A. Harney, Jessie E.  \nLangman, Tara C. Marino, Carolina Martinez,Lauren L. McKeon, Chantel  \nI.E. Moss, Sasha S. Myrie,Luke Ryan Taylor  \nDepartment of Biology, Plattsburgh State University, 101 Broad St., Plattsburgh, NY 12901  \n[Email: nancy.elwess@plattsburgh.edu](Email: nancy.elwess@plattsburgh.edu)  \n*corresponding author  \nAbstract: Alu-insertion polymorphisms were used by an undergraduate Bioinformatics class to study how these insertion sites could be the basis for an investigation in human population genetics. Based on the students’investigation, both allele and genotype Alu frequencies were determined for African-American and Japanese populations as well as a control. The three populations were tested for the presence ofAlu-insertions on the 4th, 10th and 16th chromosomes.  \nKeywords: bioinformatics, Alu insertions, SINES Introduction  \nAlu elements, short interspersed elements (SINES) have been gathering within the human genome throughout the evolution of primates. Alu elements belong to a larger group of mobile elements which compose over 45% of our DNA (Batzer & Deininger, 2002) . They are selfish pieces of DNA in that they don’t encode for any proteins, they freely replicate and finally insert themselves into new chromosomal locations. These “jumping genes” are also known as transposable DNA [transposons] and were once studied in corn by Nobel Laureate, Barbara McClintock. Alu elements are specific to the primate genome and appeared roughly 65 million years ago (Carroll et al., 200 1) . With all of the replicating and raiding of chromosomes through insertions, Alu elements make up the largest of the SINES within humans; reaching over 1 million copies per genome and making up~ 10% of the genome (Roy-Engel et al., 2001, Carroll et al., 2001) . However this being said, it should be made clear that not all Alu insertions are the same. Once an Alu element becomes‘comfortable’ in a new location, it starts to collect new mutations at the same pace as the surrounding DNA. Based on these new mutations, Alu elements are separated and organized into distinct lineages built on  \ninheritance patterns. Since each Alu insertion is secure over evolution it is inherited by basic Mendelian genetics from parent to offspring. Consequently all individuals having an Alu insertion at a specific locus share a common ancestor from which they inherited the fragment. As a result, many of these Alu insertion sites are considered “landmarks” in the evolution of the human genome (Smit, 1996; Deininger & Batzer, 1999) . Considering these factors, it was felt that the Alu-insertion polymorphisms would be an ideal topic of investigation in human population genetics for an undergraduate bioinformatics course. It was the intent of these bioinformatics’students to find differences in both the allele and genotype Alu frequencies by comparing two distinct ethnic populations (Japanese and African American) against a control. This was accomplished by using three different primers to detect specific Alu insertions on the 4th, 10th, and 16th chromosomes (Figure 1) . Here, we present an analysis of our findings for these populations using Alu insertions.  \nFigure 1. Alu Insertion Sites on Chromosomes 4, 10 and 16.Arrows represent the approximate location of the Alu insertion on the respective chromosomes (National Center for Biotechnology Information) . Figure generated by Nancy L. Elwess.  \nMethods and Materials  \nDNA Isolation Procedures (modified from the DNA Dolan Learning Center)  \nThe students had the task of collecting over 60 DNA samples, this included ~20 samples from the control group; and each of the test groups (Japanese and African-American) . The student investigators collected the samples from students on campus. Prior to the collection of samples, one liter of a 0.9% saline  \nsolution w","cbCaiu2GTPnm3BJl","https://ap.wps.com/l/cbCaiu2GTPnm3BJl","pdf",178704,"English","# Abstract\n## Keywords\n## Introduction\n## Methods and Materials\n## DNA Isolation Procedures (modified from the DNA Dolan Learning Center)\n## DNA Amplification using Polymerase Chain Reaction\n## Reagents\n## Table 1. Primer sequences","[{\"question\":\"What genomic markers does the study focus on, and why are they relevant?\",\"answer\":\"The study focuses on Alu-insertion polymorphisms, a type of short interspersed element (SINE). These insertion sites are considered informative landmarks in human genome evolution and can support population-genetics investigation.\"},{\"question\":\"Which populations and chromosome locations are compared in the analysis?\",\"answer\":\"The class compares African-American and Japanese populations against a control group. Presence of Alu insertions is tested on the 4th, 10th, and 16th chromosomes.\"},{\"question\":\"How are DNA samples prepared for downstream PCR amplification?\",\"answer\":\"Participants collect saliva-saline samples, which are concentrated and processed to obtain a DNA-containing pellet. The DNA is resuspended, treated with Chelex®, heated in a boiling water bath, then clarified by centrifugation before PCR.\"}]","Alu Insertions and Genetic Diversity - A Preliminary Investigation by an Undergraduate Bioinformatics Class | PDF",1792081129,15]