13 results on '"Cruciani, Fulvio"'
Search Results
2. Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel.
- Author
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Della Rocca C, Cannone F, D'Atanasio E, Bonito M, Anagnostou P, Russo G, Barni F, Alladio E, Destro-Bisol G, Trombetta B, Berti A, and Cruciani F
- Subjects
- Cameroon, Chad, DNA Fingerprinting, Humans, Male, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Ethnicity genetics, Genetics, Population, Haplotypes, Microsatellite Repeats, Urbanization
- Abstract
Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (Φ
ST = 0.14) largely exceeded that found among countries (ΦST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches., (Copyright © 2020 Elsevier B.V. All rights reserved.)- Published
- 2020
- Full Text
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3. A multivariate statistical approach for the estimation of the ethnic origin of unknown genetic profiles in forensic genetics.
- Author
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Alladio E, Della Rocca C, Barni F, Dugoujon JM, Garofano P, Semino O, Berti A, Novelletto A, Vincenti M, and Cruciani F
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- Discriminant Analysis, Forensic Genetics methods, Genetic Markers, Genetics, Population, Genotype, Humans, Least-Squares Analysis, Principal Component Analysis, Support Vector Machine, DNA Fingerprinting methods, Genetic Profile, Microsatellite Repeats, Racial Groups genetics
- Abstract
DNA typing and genetic profile data interpretation are among the most relevant topics in forensic science; among other applications, genetic profile's capability to distinguish biogeographic information about population groups, subgroups and affiliations have been largely explored in the last decade. In fact, for investigative and intelligence purposes, it is extremely useful to identify subjects and estimate their biogeographic origins by examining the recovered DNA profiles from evidence on a crime scene. Current approaches for BiogeoGraphic Ancestry (BGA) estimation using STRs profiles are usually based on Bayesian methods, which quantify the evidence in terms of likelihood ratio, supporting or not the hypothesis that a certain profile belongs to a specific ethnic group. The present study provides an alternative approach to the likelihood ratio method that involves multivariate data analysis strategies for the estimation of multiple populations. Starting from the well-known NIST US autosomal STRs dataset involving African-American, Asian, and Caucasian individuals, and moving towards further and more geographically restricted populations (such as Northern Africans vs sub-Saharan Africans, Afghans vs Iraqis and Italians vs Romanians), powerful multivariate techniques such as Sparse and Logistic Principal Component Analysis (SL-PCA), Sparse Partial Least Squares-Discriminant Analysis (sPLS-DA) and Support Vector Machines (SVM) were employed and their discriminating power was also compared. Both sPLS-DA and SVM techniques provided robust classifications, yielding high sensitivity and specificity models capable of discriminating populations on ethnic basis. This application may represent a powerful and dynamic tool for law enforcement agencies whenever a standard autosomal STR profile is obtained from the biological evidence collected at a crime scene or recovered during mass-disaster and missing person investigations., (Copyright © 2019 Elsevier B.V. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
4. Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa.
- Author
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D'Atanasio E, Iacovacci G, Pistillo R, Bonito M, Dugoujon JM, Moral P, El-Chennawi F, Melhaoui M, Baali A, Cherkaoui M, Sellitto D, Trombetta B, Berti A, and Cruciani F
- Subjects
- Africa, Northern, Black People genetics, DNA Fingerprinting, Genotype, Haplotypes, Humans, Male, Chromosomes, Human, Y, Genetics, Population, Microsatellite Repeats, Polymerase Chain Reaction instrumentation, Polymorphism, Single Nucleotide
- Abstract
The male-specific northern African genetic pool is characterised by a high frequency of the E-M81 haplogroup, which expanded in very recent times (2-3 kiloyears ago). As a consequence of their recent coalescence, E-M81 chromosomes often cannot be completely distinguished on the basis of their Y-STR profiles, unless rapidly-mutating Y-STRs (RM Y-STRs) are analysed. In this study, we used the Yfiler® Plus kit, which includes 7 RM Y-STRs and 20 standard Y-STR, to analyse 477 unrelated males coming from 11 northern African populations sampled from Morocco, Algeria, Libya and Egypt. The Y chromosomes were assigned to monophyletic lineages after the analysis of 72 stable biallelic polymorphisms and, as expected, we found a high proportion of E-M81 subjects (about 46%), with frequencies decreasing from west to east. We found low intra-population diversity indexes, in particular in the populations that experienced long-term isolation. The AMOVA analysis showed significant differences between the countries and between most of the 11 populations, with a rough differentiation between northwestern Africa and northeastern Africa, where the Egyptians Berbers from Siwa represented an outlier population. The comparison between the Yfiler® and the Yfiler® Plus network of the E-M81 Y chromosomes confirmed the high power of discrimination of the latter kit, thanks to higher variability of the RM Y-STRs: indeed, the number of chromosomes sharing the same haplotype was drastically reduced from 201 to 81 and limited, in the latter case, to subjects from the same population., (Copyright © 2018. Published by Elsevier B.V.)
- Published
- 2019
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5. Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries.
- Author
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Iacovacci G, D'Atanasio E, Marini O, Coppa A, Sellitto D, Trombetta B, Berti A, and Cruciani F
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- Africa, Eastern, DNA Fingerprinting, Genotype, Humans, Male, Multiplex Polymerase Chain Reaction, Mutation, Polymorphism, Single Nucleotide, Chromosomes, Human, Y, Ethnicity genetics, Genetics, Population, Microsatellite Repeats
- Abstract
By using the recently introduced 6-dye Yfiler
® Plus multiplex, we analyzed 462 males belonging to 20 ethnic groups from four eastern African countries (Eritrea, Ethiopia, Djibouti and Kenya). Through a Y-STR sequence analysis, combined with 62 SNP-based haplogroup information, we were able to classify observed microvariant alleles at four Y-STR loci as either monophyletic (DYF387S1 and DYS458) or recurrent (DYS449 and DYS627). We found evidence of non-allelic gene conversion among paralogous STRs of the two-copy locus DYF387S1. Twenty-two diallelic and triallelic patterns observed at 13 different loci were found to be significantly over-represented (p<10-6 ) among profiles obtained from cell lines compared to those from blood and saliva. Most of the diallelic/triallelic patterns from cell lines involved recurrent mutations at rapidly mutating loci (RM Y-STRs) included in the multiplex (p<10-2 ). At haplotype level, intra-population diversity indices were found to be among the lowest so far reported for the Yfiler® Plus, while statistically significant differences among countries and ethnic groups were detected when considering haplotype frequencies alone (FST ) or by using molecular distances among haplotypes (ΦST ). The strong population subdivision observed is probably the consequence of the patrilineal social organization of most eastern African ethnic groups, and suggests caution in the use of country-based haplotype frequency distributions for forensic inferences in this region., (Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.)- Published
- 2017
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6. Forensic genetic value of a 27 Y-STR loci multiplex (Yfiler(®) Plus kit) in an Italian population sample.
- Author
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Rapone C, D'Atanasio E, Agostino A, Mariano M, Papaluca MT, Cruciani F, and Berti A
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- DNA analysis, Female, Gene Frequency, Genetics, Population, Haplotypes genetics, Humans, Italy, Male, Polymerase Chain Reaction, Chromosomes, Human, Y, DNA Fingerprinting methods, Forensic Genetics methods, Microsatellite Repeats
- Abstract
The analysis of Y chromosome short tandem repeat (Y-STR) haplotypes provides important information that can be used for investigative purposes and in population studies. The Yfiler(®) Plus PCR Amplification kit (Yfiler(®) Plus, Thermo Fisher Scientific, Waltham, MA, USA) allows the multiplex amplification of 27 Y-STRs, including 7 rapidly mutating markers (RM Y-STRs). In this study, 203 unrelated males from Italy, which were subdivided into 4 different geographical groups (North, Center, South and Sardinia) were analyzed. Several intra-population diversity indexes were computed and compared to those obtained using only loci either from the minimal haplotype or the 17-plex (Yfiler(®), Thermo Fisher Scientific, Waltham, MA, USA). In addition, inter-population diversity analysis (RST) among the four Italian samples was performed. The same analysis was also used to compare the Italian sub-sets to other European populations where the Yfiler(®) Plus haplotype frequency data were available. The Sardinians were significantly differentiated from the other three Italian groups, thus requiring a specific sub-national Y-STR haplotype database. The Yfiler(®) Plus kit showed a high power of discrimination which is useful for criminal investigations, principally due to the inclusion of RM Y-STRs., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)
- Published
- 2016
- Full Text
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7. Molecular dissection of the Y chromosome haplogroup E-M78 (E3b1a): a posteriori evaluation of a microsatellite-network-based approach through six new biallelic markers.
- Author
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Cruciani F, La Fratta R, Torroni A, Underhill PA, and Scozzari R
- Subjects
- Africa, Eastern, Africa, Northern, Chromatography, High Pressure Liquid, DNA Mutational Analysis, Europe, Evolution, Molecular, Genetic Markers, Humans, Male, Middle East, Phylogeny, Polymorphism, Single Nucleotide, Chromosomes, Human, Y classification, Haplotypes, Microsatellite Repeats
- Abstract
The human Y chromosome haplogroup E-M78 (E3b1a) occurs commonly and is distributed in northern and eastern Africa, western Asia, and all of Europe. Previously, only two rarely observed internal biallelic markers (UEPs) were known within the E-M78 clade. Here we report the identification of six novel UEPs that significantly refine the phylogeny of this haplogroup. Then, we evaluate the correspondence between the newly defined sub-haplogroups and the E-M78 haplotype clusters previously identified by an 11-microsatellite loci-based network encompassing 232 chromosomes (Cruciani et al., 2004). We observed considerable correspondence between the trees generated by the two types of markers, but also noted important discrepancies between microsatellite and UEP findings. Overall, this analysis reveals that the currently visible terminal branches of the Y tree still contain a large amount of information, in terms of undiscovered biallelic markers, and that caution is needed when using the microsatellite alleles as surrogates of unique event polymorphisms.
- Published
- 2006
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8. Novel Tetranucleotide Repeat Polymorphism in the Human Adenosine Deaminase Gene: Interethnic Comparison of Three Major Human Groups
- Author
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SCOZZARI, ROSARIA, CRUCIANI, FULVIO, SANTOLAMAZZA, PIERO, PARRA, ESTEBAN, SELLITTO, DANIELE, MODIANO, DAVID, MELONI, GIANFRANCO, CAI, WANGWEI, and MORAL, PEDRO
- Published
- 1996
9. Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication.
- Author
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Ravasini, Francesco, D'Atanasio, Eugenia, Bonito, Maria, Bonucci, Biancamaria, Della Rocca, Chiara, Berti, Andrea, Trombetta, Beniamino, and Cruciani, Fulvio
- Subjects
Y chromosome ,MICROSATELLITE repeats ,CLUSTER analysis (Statistics) ,CHROMOSOMAL rearrangement ,FORENSIC genetics ,MALE infertility - Abstract
The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the AZFc. In a previous study, we identified four phylogenetically related samples with a null allele at DYS448 and a tetrallelic pattern at DYF387S1, two Y-STRs located in the AZFc. Through NGS read depth analysis, we found that the unusual Y-STR pattern may be due to a 1.6 Mb deletion arising concurrently or after a 3.5 Mb duplication event. The observed large genomic rearrangement results in copy number reduction for the RBMY gene family as well as duplication of other AZFc genes. Based on the diversity of 16 additional Y-STRs, we estimated that the duplication/deletion event occurred at least twenty generations ago, suggesting that it has not been affected by negative selection. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
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10. Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages
- Author
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Cruciani, Fulvio, Trombetta, Beniamino, Daniele, Sellitto, Massaia, Andrea, DESTRO-BISOL, Giovanni, Elizabeth, Watson, Colomb, E. B., Eliane Beraud Colomb, Jean Michel Dugoujon, Pedro, Moral, and Scozzari, Rosaria
- Subjects
Male ,Haplogroup L4a ,Haplogroup M ,Asia ,Time Factors ,Letter ,Chad ,Human Y-chromosome DNA haplogroup ,Biology ,Article ,Haplogroup ,Fathers ,Africa, Northern ,y chromosome haplogroups ,Genetics ,Humans ,Haplogroup D-M15 ,Genetics (clinical) ,Phylogeny ,Language ,Chromosomes, Human, Y ,Geography ,chadic-speaking populations ,Haplogroup L3 ,Emigration and Immigration ,Haplogroup IJ ,human migrations ,eye diseases ,Y-chromosomal Adam ,africa ,Haplotypes ,holocene ,Evolutionary biology ,Microsatellite Repeats - Abstract
Although human Y chromosomes belonging to haplogroup R1b are quite rare in Africa, being found mainly in Asia and Europe, a group of chromosomes within the paragroup R-P25(*) are found concentrated in the central-western part of the African continent, where they can be detected at frequencies as high as 95%. Phylogenetic evidence and coalescence time estimates suggest that R-P25(*) chromosomes (or their phylogenetic ancestor) may have been carried to Africa by an Asia-to-Africa back migration in prehistoric times. Here, we describe six new mutations that define the relationships among the African R-P25(*) Y chromosomes and between these African chromosomes and earlier reported R-P25 Eurasian sub-lineages. The incorporation of these new mutations into a phylogeny of the R1b haplogroup led to the identification of a new clade (R1b1a or R-V88) encompassing all the African R-P25(*) and about half of the few European/west Asian R-P25(*) chromosomes. A worldwide phylogeographic analysis of the R1b haplogroup provided strong support to the Asia-to-Africa back-migration hypothesis. The analysis of the distribution of the R-V88 haplogroup in1800 males from 69 African populations revealed a striking genetic contiguity between the Chadic-speaking peoples from the central Sahel and several other Afroasiatic-speaking groups from North Africa. The R-V88 coalescence time was estimated at 9.2-5.6 [corrected] kya, in the early mid Holocene. We suggest that R-V88 is a paternal genetic record of the proposed mid-Holocene migration of proto-Chadic Afroasiatic speakers through the Central Sahara into the Lake Chad Basin, and geomorphological evidence is consistent with this view.
- Published
- 2010
11. Improving discrimination capacity through rapidly mutating Y-STRs in structured populations from the African continent.
- Author
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Della Rocca, Chiara, Trombetta, Beniamino, Barni, Filippo, D'Atanasio, Eugenia, Hajiesmaeil, Mogge, Berti, Andrea, Hadi, Sibte, and Cruciani, Fulvio
- Subjects
TANDEM repeats ,LOCUS (Genetics) ,MICROSATELLITE repeats ,Y chromosome ,HAPLOTYPES ,AFRICANS - Abstract
Y chromosome short tandem repeats (Y-STRs) typing is becoming increasingly popular in forensic casework mainly because it allows the recovery of male-specific genetic information from severely unbalanced male-female DNA mixtures. The relatively low discrimination power of conventional Y-STR multiplexes, due to linkage disequilibrium among polymorphic loci, has been partially overcome by the introduction of rapidly mutating Y microsatellites (RM Y-STRs) with mutation rates exceeding 1 × 10
-2 /generation. In previous works, we reported an unexpectedly high level of haplotype sharing among African males using the Yfiler Plus PCR Amplification kit, the most powerful commercially available system, including 19 conventional Y-STRs and 6 RM Y-STRs. In particular, analyzing 1370 males from northern, eastern and central Africa, 240 subjects were found to share 100 Y-STR haplotypes. We attributed the relatively low discrimination capacity to several factors including patrilocality, endogamy, sampling bias and degree of urbanization. In the present study, using a blind search analysis based on 16 autosomal STRs, we first investigated the kinship between pairs of African males previously found to share the Yfiler Plus haplotype; then, we evaluated the improvement in identification capacity allowed by a PCR multiplex assay (RM-YPlex) based on 13 "first generation" RM Y-STR, seven of which are not included in the Yfiler Plus multiplex. Among 228 pairs of males sharing a Yfiler Plus haplotype, we detected 134 related (cousins or closer) and 94 unrelated (or distantly related) pairs of subjects. By using the RM-YPlex, we observed a full genotype concordance for the six loci shared with the Yfiler Plus, while the additional seven RM Y-STRs allowed the discrimination among 58.2 % related pairs and 84.0 % unrelated pairs. The discrimination capacity increased from 0.898 to 0.958, while the proportion of males sharing a haplotype decreased from 17.5 % to 8.0 %. These findings further highlight the capability of RM Y-STRs to distinguish males even in close kinship scenarios and in sub-structured populations as African ones, but at the same time call for the discovery and testing of additional RM Y-STRs to fully differentiate male relatives. • Discrimination power of RM Y-STRs in endogamous African populations was investigated. • Low discrimination power previously observed is only partially due to close kinship. • Discrimination capacity increased from 0.898 (Yfiler Plus) to 0.958 using RM Y-STRs. • Additional RM Y-STRs are required to fully differentiate male relatives. [ABSTRACT FROM AUTHOR]- Published
- 2022
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12. Combined Use of Biallelic and Microsatellite Y-Chromosome Polymorphisms to Infer Affinities among African Populations.
- Author
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Scozzari, Rosaria, Cruciani, Fulvio, Santolamazza, Piero, Malaspina, Patrizia, Torroni, Antonio, Sellitto, Daniele, Arredi, Barbara, Destro-Bisol, Giovanni, Biondi, Gianfranco, Moral, Pedro, Olckers, Antonel, Wallace, Douglas C., and Novelletto, Andrea
- Subjects
- *
MICROSATELLITE repeats , *GENETIC polymorphisms - Abstract
Examines the genetic affinities of biallelic and microsatellite of Y chromosome polymorphism among African populations. Combination of dinucleotide-repeat polymorphism in establishing Y chromosome compound superhaplotypes; Distribution of microsatellites within haplotype; Diversity of Y chromosomal biallelic haplotypes.
- Published
- 1999
- Full Text
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13. The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time.
- Author
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Zhivotovsky, Lev A., Underhill, Peter A., Cinnio&gcaron;lu, Cengiz, Kayser, Manfred, Morar, Bharti, Kivisild, Toomas, Scozzari, Rosaria, Cruciani, Fulvio, Destro-Bisol, Giovanni, Spedini, Gabriella, Chambers, Geoffrey K., Herrera, Rene J., Kiau Kiun Yong, Gresham, David, Tournev, Ivailo, Feldman, Marcus W., and Kalaydjieva, Luba
- Subjects
- *
MICROSATELLITE repeats , *HUMAN chromosomes , *GENETIC polymorphisms , *HUMAN molecular genetics , *LINKAGE (Genetics) , *HUMAN population genetics - Abstract
We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9 x 10[sup-4] per 25 years, with a standard deviation across loci of 5.7 x 10[sup-4], using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria. [ABSTRACT FROM AUTHOR]
- Published
- 2004
- Full Text
- View/download PDF
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