scholarly journals Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research

2021 ◽  
Vol 12 ◽  
Author(s):  
Carla Bini ◽  
Elisabetta Cilli ◽  
Stefania Sarno ◽  
Mirko Traversari ◽  
Francesco Fontani ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Tandem Repeats ◽  
18Th Century ◽  
Dna Typing ◽  
Geographical Location ◽  
Pcr Amplification ◽  
Petrous Bone ◽  
Qualitative Assessment ◽  
The Village ◽  
Short Tandem

Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent’s criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.

Population Genetics of Y-Chromosome Short Tandem Repeats in Humans

1997 ◽  
Vol 45 (3) ◽  
pp. 265-270 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
Mark Seielstad ◽  
Eva Mateu ◽  
David Comas ◽  
...  
Keyword(s):  
Population Genetics ◽  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals Sex-Specific Migration Patterns in Central Asian Populations, Revealed by Analysis of Y-Chromosome Short Tandem Repeats and mtDNA

1999 ◽  
Vol 65 (1) ◽  
pp. 208-219 ◽  
Author(s):  
Anna Pérez-Lezaun ◽  
Francesc Calafell ◽  
David Comas ◽  
Eva Mateu ◽  
Elena Bosch ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Migration Patterns ◽  
Asian Populations ◽  
Central Asian ◽  
Short Tandem

scholarly journals Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples

2018 ◽  
Vol 2018 ◽  
pp. 1-5
Author(s):  
Fidelis Charles Bugoye ◽  
Elias Mulima ◽  
Gerald Misinzo
Keyword(s):  
Y Chromosome ◽  
Mutation Rate ◽  
Standard Error ◽  
Tandem Repeats ◽  
Dna Typing ◽  
Paternity Testing ◽  
Mutation Rates ◽  
Buccal Swab ◽  
Age Difference ◽  
Rate Analysis

Hundred unrelated father-son buccal swab sample pairs collected from consented Tanzanian population were examined to establish mutation rates using 17 Y-STRs loci DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4 of the AmpFlSTRYfiler kit used in forensics and paternity testing. Prior to 17 Y-STRs analysis, father-son pair biological relationships were confirmed using 15 autosomal STRs markers and found to be paternally related. A total of four single repeat mutational events were observed between father and sons. Two mutations resulted in the gain of a repeat and the other two resulted in a loss of a repeat in the son. All observed mutations occurred at tetranucleotide loci DYS389II, DYS385a, and DYS385b. The locus specific mutation rate varied between 0 and 1.176 x10−3 and the average mutation rate of 17Y-STRs loci in the present study was 2.353x10−3 (6.41x10−4 - 6.013x10−3) at 95% CI. Furthermore the mean fathers’ age with at least one mutation at son’s birth was 32 years with standard error of 2.387 while the average age of all fathers without mutation in a sampled population at son’s birth was 26.781 years with standard error of 0.609. The results shows that fathers’ age at son’s birth may have an effect on Y-STRs mutation rate analysis, though this age difference was statistically not significant using unpaired samples t-test (p = 0.05). As a consequence of observed mutation rates in this study, the precise and reliable understanding of mutation rate at Y-chromosome STR loci is necessary for a correct evaluation and interpretation of DNA typing results in forensics and paternity testing involving males. The criterion for exclusion in paternity testing should be defined, so that an exclusion from paternity has to be based on exclusion constellations at a minimum of two 17 Y-STRs loci.

Y chromosome genetic data defined by 23 short tandem repeats in a Serbian population on the Balkan Peninsula

2019 ◽  
Vol 46 (1) ◽  
pp. 77-83
Author(s):  
Tamara Kačar ◽  
Gorana Stamenković ◽  
Jelena Blagojević ◽  
Jovica Krtinić ◽  
Dragan Mijović ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Genetic Data ◽  
Balkan Peninsula ◽  
Short Tandem

US forensic Y-chromosome short tandem repeats database

2010 ◽  
Vol 12 (6) ◽  
pp. 289-295 ◽  
Author(s):  
Jianye Ge ◽  
Bruce Budowle ◽  
John V. Planz ◽  
Arthur J. Eisenberg ◽  
Jack Ballantyne ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals Variation in Short Tandem Repeats Is Deeply Structured by Genetic Background on the Human Y Chromosome

1999 ◽  
Vol 65 (6) ◽  
pp. 1623-1638 ◽  
Author(s):  
Elena Bosch ◽  
Francesc Calafell ◽  
Fabrício R. Santos ◽  
Anna Pérez-Lezaun ◽  
David Comas ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Genetic Background ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Human Y Chromosome ◽  
Short Tandem

scholarly journals A Short Tandem Repeat Assay for Studying Genetic Variation in Madurella mycetomatis (MmySTR)

2020 ◽  
Author(s):  
Bertrand Nyuykonge ◽  
Kimberly Eadie ◽  
Willemien H. A. Zandijk ◽  
Sarah A. Ahmed ◽  
Marie Desnos-Ollivier ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Tandem Repeats ◽  
Diversity Index ◽  
Clinical Manifestations ◽  
Pcr Amplification ◽  
Reference Database ◽  
Madurella Mycetomatis ◽  
Typing Technique ◽  
Short Tandem ◽  
D Value

Introduction: Madurella mycetomatis is the major causative agent of eumycetoma, a neglected tropical infection characterized by painless subcutaneous lesions, inflammation and grains draining from multiple sinuses. To study the epidemiology of mycetoma, a robust discriminatory typing technique is needed. We describe the use of a Short Tandem Repeats assay (MmySTR) for genotyping of M. mycetomatis isolates predominantly from Sudan. Methods: Eleven microsatellite markers (3 dinucleotides, 4 trinucleotide repeats and 4 tetranucleotide repeats) were selected from the M. mycetomatis MM55 genome using the Tandem Repeats Finder software. PCR amplification primers were designed for each microsatellite marker using primer3 software and amplified in a multicolor multiplex PCR approach. To establish the extent of genetic variation within the population, a collection of 120 clinical isolates from different regions was genotyped with this assay. Results: The 11 selected MmySTR markers showed a large genotypic heterogeneity. From a collection of 120 isolates, 108 different genotypes were obtained. The Simpsons’ diversity index (D) value for individual markers ranged from 0.081-0.881, the combined panel displayed an overall D value of 0.997. The MmySTR assay demonstrated high stability, reproducibility and specificity. Conclusion: The MmySTR assay is a promising new typing technique that can be used to genotype isolates of M. mycetomatis. Apart from the possible contribution of host factors, the genetic diversity observed among this group of isolates might contribute to the different clinical manifestations of mycetoma. We recommend the MmySTR assay to be used to establish a global reference database for future study of M. mycetomatis isolates.

scholarly journals Determining the Genetic Similarities and Variability of Javanese and Arab Ethnic Families with DNA Fingerprint in Malang East Java Indonesia

2017 ◽  
Vol 17 (1) ◽  
pp. 51
Author(s):  
Nila Kartika Sari
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Tandem Repeats ◽  
Pcr Amplification ◽  
Dna Fingerprint ◽  
Salting Out ◽  
Breeding Populations ◽  
Human White Blood Cell ◽  
And Migration ◽  
Short Tandem

PENENTUAN SIMILARITAS DAN VARIABILITAS GENETIK PADA KELUARGA ETNIS JAWA DAN ARAB DENGAN DNA FINGERPRINT DI MALANG, JAWA TIMUR, INDONESIA ABSTRAKLebih dari sepertiga genom manusia terdiri dari urutan daerah berulang (Repeat area) yang terdiri dari Minisatellite atau Variant Number Of Tandem Repeats (VNTR) dan Microsatellite atau Short Tandem Repeat (STR). STR sebagai daerah berulang dengan rentang alel yang pendek sering digunakan untuk tes paternitas, penelitian penyakit genetik dalam bidang kesehatan, arkeologi molekular, maupun kasus kriminalitas dalam bidang forensic. Tujuan dari penelitian ini adalah untuk mengidentifikasi DNA Fingerprint pada etnis Jawa – Arab dengan menentukan similaritas dan variabilitas genetiknya. Bahan dan metode yang digunakan untuk mengerjakan adalah menggunakan sel darah putih manusia yang berasal dari tiga generasi dalam tiga keluarga yang terdiri dari : (1) Nenek – Ibu, Ayah – anak perempuan, (2) Kakek – Ibu, Ayah – Anak perempuan, (3) Kakek, Nenek – Ibu, Ayah – Anak laki-laki. Isolasi DNA pada tiap sampel diperoleh dengan salting out, selanjutnya Amplifikasi PCR dengan menggunakan 13 CODIS yang meliputi TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 dan amelogenin yang dapat dilihat melalui hasil elektroforesis gel poliakrilamid 8% dengan Chemidoc Gel Imaging. Analisis profil pita pada tiap individu untuk menentukan similaritas dan variabilitas genetik serta pola alel dengan menggunakan software Quantity One. Variasi pola pita DNA dianalisis dengan menggunakan program software GENEPOP package versi 4.2 yang akan didapat frekuensi alel, heterozigositas, dan migrasi alel. Berdasarkan identifikasi yang dilakukan diperoleh bahwa nilai heterozigositas pada populasi III (93.8461%) memiliki nilai heterozigositas lebih tinggi dibandingkan dengan populasi I (88.4615%) dan II (76.9230%) dan telah terjadi migrasi alel 0.341373%.  Adanya persentase migrasi alel tersebut meskipun kecil menunjukkan telah terjadi Breeding diantara populasi Jawa dengan populasi Arab sehingga meningkatkan rata-rata nilai heterozigositas pada tiap populasi. Pola alel heterozigot dengan berdasarkan nilai heterozigositas, jumlah alel pada D21S11, VWA dan THO1 dapat direkomendasikan sebagai penanda molekular untuk identifikasi variasi genetik.Kata kunci: Etnis Jawa–Arab, DNA Fingerprint, 13 CODIS DETERMINING THE GENETIC SIMILARITIES AND VARIABILITY OF JAVANESE AND ARAB ETHNIC FAMILIES WITH DNA FINGERPRINT IN MALANG EAST JAVA INDONESIAABSTRACTMore than one-third of human genome consists of repetitive sequence region (Repeat Area) which consist of Minisatellite or Variant Number Of Tandem Repeats (VNTR) and Microsatellite or Short Tandem Repeat (STR). Based on its short allele range STR can be used for the paternity testing study of genetics disease, molecular archeology, as well as in forensic crime cases. The aim of this study is to identify Javanese – Arab Ethnic DNA fingerprint in determining the similarities and genetic variability. Materials and methods to accomplish this, we used human white blood cell from three generations of three family consists of: (1) grandmother-mother, father-daughter, (2) grandfather-mother, father-daughter, (3) grandfather, grandmother–mother, father-son. DNA blood samples were Isolated by salting out, furthermore PCR amplification used by applying 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 and amelogenin, and then it was visualized by 8% polyacrylamid gel. The Fingerprint profile was visualized by 8% polyacrylamide gel and took the picture by ChemiDoc gel Imaging and measure the intensity band pattern by Quantity One software. Variations in the pattern of DNA bands were analyzed using the program GENEPOP software package version 4.2 that will be obtained allele frequencies, heterozygosity, and allele migration. Based on identification, this result showed analysis heterozygosity values, population III (93.8461%) have higher heterozygosity values compared with the population I (88.4615%) and II (76.9230%) and migration of alleles 0.341373%. The percentage of the migration though minor allele had occurred Breeding populations between Java to the Patterns of heterozygous alleles with values based on heterozygosity, number of alleles at D21S11,VWA and THO1 can be recommended as a molecular marker for the identification of genetic variation.Keywords: Javanese – Arab Ethnics, DNA fingerprint, 13 CODIS

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