Publications by authors named "Daniele Podini"

20 Publications

  • Page 1 of 1

Population genetic data of 74 microhaplotypes in four major U.S. population groups.

Forensic Sci Int Genet 2020 Nov 3;49:102398. Epub 2020 Oct 3.

The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC, 20007, United States. Electronic address:

Microhaplotypes (microhaps or MHs) are novel forensically relevant genetic markers that demand large and appropriate allele frequency datasets for their implementation in casework. In this study we report on the allele frequency data of 74 microhap loci (230 SNPs) included in a newly developed 74-plex assay. The panel was tested on the Ion S5 system on a total of 347 samples from four main U.S. population groups of African, European, East Asian and Southwest Hispanic descent. Overall, frequencies of individual alleles at each locus varied considerably among the different population groups. An increase in the average value of gene diversity was also observed as the number of SNPs per locus increased. Most microhap markers showed no significant deviation from Hardy-Weinberg ratios within any of the individual population samples displaying an average power of discrimination between 0.74 and 0.81 and an average probability of exclusion between 0.32 and 0.39. Moreover, the four population groups had no clear genetic affinities with the exception of U.S. European and U.S. Southwest Hispanic populations, which showed the lowest F value. STRUCTURE and principal component analyses (PCA) analysis resulted in effective clustering of the four populations with the U.S. European and Southwest Hispanic showing some overlap. These results support the potential use of this sequence-based 74plex-microhaplotype assay for ancestry inference in addition to previously reported human identification and mixture deconvolution capabilities.
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http://dx.doi.org/10.1016/j.fsigen.2020.102398DOI Listing
November 2020

Novel mutation identification and copy number variant detection via exome sequencing in congenital muscular dystrophy.

Mol Genet Genomic Med 2020 11 16;8(11):e1387. Epub 2020 Sep 16.

Department of Pharmacology and Physiology, Institute for Neuroscience, The George Washington University, Washington, DC, USA.

Background: Congenital muscular dystrophy type 1A (MDC1A), also termed merosin-deficient congenital muscular dystrophy (CMD), is a severe form of CMD caused by mutations in the laminin α2 gene (LAMA2). Of the more than 300 likely pathogenic variants found in the Leiden Open Variant Database, the majority are truncating mutations leading to complete LAMA2 loss of function, but multiple copy number variants (CNVs) have also been reported with variable frequency.

Methods: We collected a cohort of individuals diagnosed with likely MDC1A and sought to identify both single nucleotide variants and small and larger CNVs via exome sequencing by extending the analysis of sequencing data to detect splicing changes and CNVs.

Results: Standard exome analysis identified multiple novel LAMA2 variants in our cohort, but only four cases carried biallelic variants. Since likely truncating LAMA2 variants are often found in heterozygosity without a second allele, we performed additional splicing and CNV analysis on exome data and identified one splice change outside of the canonical sequences and three CNVs, in the remaining four cases.

Conclusions: Our findings support the expectation that a portion of MDC1A cases may be caused by at least one CNV allele and show how these changes can be effectively identified by additional analysis of existing exome data.
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http://dx.doi.org/10.1002/mgg3.1387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667317PMC
November 2020

A sequence-based 74plex microhaplotype assay for analysis of forensic DNA mixtures.

Forensic Sci Int Genet 2020 Nov 11;49:102367. Epub 2020 Aug 11.

The George Washington University, Department of Forensic Science, 2100 Foxhall Road, NW, Washington, DC, 20007, United States. Electronic address:

Microhaplotypes are emerging biomarkers for forensic applications. In this study, a sequence-based multiplex assay of 74 microhaplotypes (230 SNPs) was developed on the Ion Torrent S5™ (Thermo Fisher Scientific) system and the potential for its application to mixture deconvolution was explored. The 74 loci are distributed across the autosomal human genome and have A (i.e., effective number of alleles) values ranging from 1.307 to 6.010 (median = 2.706) and I (i.e., informativeness) values ranging from 0.096 to 0.660 (median = 0.251); the amplicon sizes range between 157 and 325 bp. The typing performance of the panel was evaluated on a series of in-silico two to five-person DNA mixtures and results were compared to fragment and sequence-based STRs. The 74plex-locus assay was found sensitive down to 0.05 ng of input DNA and effective for the analysis of mixtures at different contributor ratios and input DNA amounts. As expected, none or very partial minor CE-STR profile(s) were reported for highly imbalanced two-person and high-order DNA mixtures while sequencing of STRs enabled the detection of more individual minor alleles. For microhaplotypes, a full minor profile was detected down to a 20:1 ratio at 10 ng and minimal allele dropout at 1 ng of input DNA. A higher rate of allele dropout from the minor donor(s) was reported at 1 ng than 10 ng for three-person mixtures while for four- and five-person mixtures, the same number of dropouts was observed for almost all minor donors. Overall this microhaplotype panel is a powerful tool that can complement and enhance size- and sequence-based STR analysis of forensic DNA mixtures.
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http://dx.doi.org/10.1016/j.fsigen.2020.102367DOI Listing
November 2020

Forensic molecular biomarkers for mixture analysis.

Forensic Sci Int Genet 2019 07 30;41:107-119. Epub 2019 Apr 30.

Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC 20007, United States.

The deconvolution of DNA mixtures has gathered the attention of forensic DNA scientists for over two decades. To enhance mixture deconvolution capabilities, a new generation of sensitive DNA-typing approaches has been recently proposed. In this review, we describe novel, forensically relevant multi-SNP loci (i.e., microhaplotypes or microhaps), compound markers (i.e., DIP-STRs, SNP-STRs and DIP-SNPs) and lineage markers (i.e., rapidly mutating Y chromosome STRs) that improve the deconvolution of two and more than two-person mixtures typed using conventional STR, binary and non-binary loci. We explore the features and applications of these emerging molecular biomarkers with respect to their ability to forensically detect same-or-opposite sex donors. Finally, we discuss the impact of initial massively parallel sequencing (MPS) investigations of STR, microhaplotype and SNP/indel assays for DNA mixture profiling.
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http://dx.doi.org/10.1016/j.fsigen.2019.04.003DOI Listing
July 2019

Correction to: Mixture deconvolution by massively parallel sequencing of microhaplotypes.

Int J Legal Med 2019 05;133(3):731

The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA.

The original version of this article contained an author name error. In this article, Katrina Madella has been corrected to Katrina Maddela.
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http://dx.doi.org/10.1007/s00414-019-02031-2DOI Listing
May 2019

Mixture deconvolution by massively parallel sequencing of microhaplotypes.

Int J Legal Med 2019 05 13;133(3):719-729. Epub 2019 Feb 13.

The Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, D.C., 20007, USA.

Short tandem repeat polymorphisms (STRs) are the standard markers for forensic human identification. STRs are highly polymorphic loci analyzed using a direct PCR-to-CE (capillary electrophoresis) approach. However, STRs have limitations particularly when dealing with complex mixtures. These include slippage of the polymerase during amplification causing stutter fragments that can be indistinguishable from minor contributor alleles, preferential amplification of shorter alleles, and limited number of loci that can be effectively co-amplified with CE. Massively parallel sequencing (MPS), by enabling a higher level of multiplexing and actual sequencing of the DNA, provides forensic practitioners an increased power of discrimination offered by the sequence of STR alleles and access to new sequence-based markers. Microhaplotypes (i.e., microhaps or MHs) are emerging multi-allelic loci of two or more SNPs within < 300 bp that are highly polymorphic, have alleles all of the same length, and do not generate stutter fragments. The growing number of loci described in the literature along with initial mixture investigations supports the potential for microhaps to aid in mixture interpretation and the purpose of this study was to demonstrate that practically. A panel of 36 microhaplotypes, selected from a set of over 130 loci, was tested with the Ion S5™ MPS platform (Thermo Fisher Scientific) on single-source samples, synthetic two-to-six person mixtures at different concentrations/contributor ratios, and on crime scene-like samples. The panel was tested both in multiplex with STRs and SNPs and individually. The analysis of single-source samples showed that the allele coverage ratio across all loci was 0.88 ± 0.08 which is in line with the peak height ratio of STR alleles in CE. In mixture studies, results showed that the input DNA can be much higher than with conventional CE, without the risk of oversaturating the detection system, enabling an increased sensitivity for the minor contributor in imbalanced mixtures with abundant amounts of DNA. Furthermore, the absence of stutter fragments simplifies the interpretation. On casework-like samples, MPS of MHs enabled the detection of a higher number of alleles from minor donors than MPS and CE of STRs. These results demonstrated that MPS of microhaplotypes can complement STRs and enhance human identification practices when dealing with complex imbalanced mixtures.
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http://dx.doi.org/10.1007/s00414-019-02010-7DOI Listing
May 2019

Microhaplotypes in forensic genetics.

Forensic Sci Int Genet 2019 01 1;38:54-69. Epub 2018 Oct 1.

Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC, 20007, United States. Electronic address:

Microhaplotype loci (microhaps, MHs) are a novel type of molecular marker of less than 300 nucleotides, defined by two or more closely linked SNPs associated in multiple allelic combinations. The value of these markers is enhanced by massively parallel sequencing (MPS), which allows the sequencing of both parental haplotypes at each of the many multiplexed loci. This review describes the features of these multi-SNP markers and documents their value in forensic genetics, focusing on individualization, biogeographic ancestry inference, and mixture deconvolution. Foreseeable applications also include missing person identification, relationship testing, and medical diagnostic applications. The technique is not restricted to humans.
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http://dx.doi.org/10.1016/j.fsigen.2018.09.009DOI Listing
January 2019

Proximity Ligation Real-Time PCR: A protein-based confirmatory method for the identification of semen and sperm cells from sexual assault evidence.

Forensic Sci Int Genet 2018 11 25;37:64-72. Epub 2018 Jul 25.

Department of Forensic Sciences, The George Washington University, 2100 Foxhall Road NW, Washington, DC 20007, USA.

The positive identification of seminal fluids in sexual assault crimes is considered crucial evidence to determine whether a sexual act occurred or not. However, current presumptive methods lack specificity and sensitivity. Confirmation of semen by microscopic examination of spermatozoa is laborious, time consuming, and can sometimes lead to negative or inconclusive results. Here we report the use of the Proximity Ligation Real-Time PCR (PLiRT-PCR) assay as an attractive and promising confirmatory method for the identification of semen and sperm proteins using two polyclonal antibodies, Prostate Specific Antigen (PSA) and Sperm-Specific Protein (SP10), respectively. PLiRT-PCR, relies on protein recognition by pairs of proximity probes (antibody-DNA conjugates) that give rise to a ligated DNA strand. The ligated DNA strand is then amplified and detected by qPCR.
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http://dx.doi.org/10.1016/j.fsigen.2018.07.019DOI Listing
November 2018

Correction to: Population data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria.

Int J Legal Med 2018 05;132(3):739

Department of Forensic Sciences, The George Washington University, Washington, DC, USA.

In the original paper author Alani Sulaimon Akanmu was erroneously omitted from the author list. Prof. Akanmu has now been added as 4 author. Prof. Akanmu acted as an academic supervisor of the study and additionally contributed to the publication by reading, commenting and editing the manuscript.
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http://dx.doi.org/10.1007/s00414-018-1779-7DOI Listing
May 2018

Population data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria.

Int J Legal Med 2018 05 4;132(3):735-737. Epub 2017 Nov 4.

Department of Forensic Sciences, The George Washington University, Washington, DC, USA.

The three major ethnic groups of Nigerian population namely the Hausa, Igbo and Yoruba make up 29, 21 and 18% of the total population, respectively. To provide genetic information necessary for forensic analysis, this study was carried out to determine STR allele frequencies in 102 Hausa, 128 Igbo and 134 Yoruba individuals in Nigeria using 21 STR loci including the 20 CODIS (Combined DNA Index System) loci plus SE33.
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http://dx.doi.org/10.1007/s00414-017-1722-3DOI Listing
May 2018

Evaluating 130 microhaplotypes across a global set of 83 populations.

Forensic Sci Int Genet 2017 07 16;29:29-37. Epub 2017 Mar 16.

Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT, 06520-8005, USA.

Today the primary DNA markers used in forensics are short tandem repeat (STR) polymorphisms (STRPs), initially selected because they are highly polymorphic. However, the increasingly common need to deal with samples with a mixture of DNA from two or more individuals sometimes is complicated by the inherent stutter involved with PCR amplification, especially in strongly unbalanced mixtures when the minor component coincides with the stutter range of the major component. Also, the STRPs in use provide little evidence of ancestry of a single source sample beyond broad "continental" resolution. Methodologies for analyzing DNA have become much more powerful in recent years. Massively parallel sequencing (MPS) is a new method being considered for routine use in forensics. Primarily to aid in mixture deconvolution and avoid the issue of stutter, we have begun to investigate a new type of forensic marker, microhaplotype loci, that will provide useful information on mixtures of DNA and on ancestry when typed using massively parallel sequencing (MPS). We have identified 130 loci and estimated their haplotype (allele) frequencies in 83 different population samples. Many of these loci are shown to be highly informative for individual identification and for mixture identification and deconvolution.
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http://dx.doi.org/10.1016/j.fsigen.2017.03.014DOI Listing
July 2017

Short tandem repeats, segmental duplications, gene deletion, and genomic instability in a rapidly diversified immune gene family.

BMC Genomics 2016 11 9;17(1):900. Epub 2016 Nov 9.

The Department of Biological Sciences, George Washington University, Washington, DC, USA.

Background: Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence. Consequently, we have resolved the structure of the family and profiled the members by sequencing selected BAC clones using Illumina and PacBio approaches.

Results: BAC insert assemblies identified 15 predicted genes that are organized into three clusters. Two of the gene clusters have almost identical flanking regions, suggesting that they may be non-matching allelic clusters residing at the same genomic locus. GA STRs surround all genes and appear in large stretches at locations of putatively deleted genes. GAT STRs are positioned at the edges of segmental duplications that include a subset of the genes. The unique locations of the STRs suggest their involvement in gene deletions and segmental duplications. Genomic profiling of the Sp185/333 gene diversity in 10 sea urchins shows that no gene repertoires are shared among individuals indicating a very high gene diversification rate for this family.

Conclusions: The repetitive genomic structure of the Sp185/333 family that includes STRs in strategic locations may serve as platform for a controlled mechanism which regulates the processes of gene recombination, gene conversion, duplication and deletion. The outcome is genomic instability and allelic mismatches, which may further drive the swift diversification of the Sp185/333 gene family that may improve the immune fitness of the species.
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http://dx.doi.org/10.1186/s12864-016-3241-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103432PMC
November 2016

The Potential Use of Forensic DNA Methods Applied to Sand Fly Blood Meal Analysis to Identify the Infection Reservoirs of Anthroponotic Visceral Leishmaniasis.

PLoS Negl Trop Dis 2016 05 18;10(5):e0004706. Epub 2016 May 18.

The Department of Forensic Sciences, Columbian College of Arts & Sciences, George Washington University, Washington, D.C., United States of America.

Background: In the Indian sub-continent, visceral leishmaniasis (VL), also known as kala azar, is a fatal form of leishmaniasis caused by the kinetoplastid parasite Leishmania donovani and transmitted by the sand fly Phlebotomus argentipes. VL is prevalent in northeast India where it is believed to have an exclusive anthroponotic transmission cycle. There are four distinct cohorts of L. donovani exposed individuals who can potentially serve as infection reservoirs: patients with active disease, cured VL cases, patients with post kala azar dermal leishmaniasis (PKDL), and asymptomatic individuals. The relative contribution of each group to sustaining the transmission cycle of VL is not known.

Methodology/principal Findings: To answer this critical epidemiological question, we have addressed the feasibility of an approach that would use forensic DNA methods to recover human DNA profiles from the blood meals of infected sand flies that would then be matched to reference DNA sampled from individuals living or working in the vicinity of the sand fly collections. We found that the ability to obtain readable human DNA fingerprints from sand flies depended entirely on the size of the blood meal and the kinetics of its digestion. Useable profiles were obtained from most flies within the first 24 hours post blood meal (PBM), with a sharp decline at 48 hours and no readable profiles at 72 hours. This early time frame necessitated development of a sensitive, nested-PCR method compatible with detecting L. donovani within a fresh, 24 hours blood meal in flies fed on infected hamsters.

Conclusion/significance: Our findings establish the feasibility of the forensic DNA method to directly trace the human source of an infected blood meal, with constraints imposed by the requirement that the flies be recovered for analysis within 24 hours of their infective feed.
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http://dx.doi.org/10.1371/journal.pntd.0004706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871566PMC
May 2016

Genomics in premature infants: a non-invasive strategy to obtain high-quality DNA.

Sci Rep 2014 Mar 6;4:4286. Epub 2014 Mar 6.

1] Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Health System, 111 Michigan Avenue NW, Washington, DC; USA [2] Department of Pediatrics, George Washington University School of Medicine, Washington, DC; USA.

We used a cost-effective, non-invasive method to obtain high-quality DNA from buccal epithelial-cells (BEC) of premature infants for genomic analysis. DNAs from BEC were obtained from premature infants with gestational age ≤ 36 weeks. Short terminal repeats (STRs) were performed simultaneously on DNA obtained from the buccal swabs and blood from the same patient. The STR profiles demonstrated that the samples originated from the same individual and exclude any contamination by external DNAs. Whole exome sequencing was performed on DNAs obtained from BEC on premature infants with and without necrotizing enterocolitis, and successfully provided a total number of reads and variants corroborating with those obtained from healthy blood donors. We provide a proof of concept that BEC is a reliable and preferable source of DNA for high-throughput sequencing in premature infants.
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http://dx.doi.org/10.1038/srep04286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944721PMC
March 2014

Forensic interlaboratory evaluation of the ForFLUID kit for vaginal fluids identification.

J Forensic Leg Med 2014 Jan 5;21:60-3. Epub 2013 Nov 5.

University of Rome "Foro Italico", Department of Movement, Human and Health Sciences, Public Health Unit, P.zza L. De Bosis, 6, 00135 Rome, Italy. Electronic address:

Identification of vaginal fluids is an important step in the process of sexual assaults confirmation. Advances in both microbiology and molecular biology defined technical approaches allowing the discrimination of body fluids. These protocols are based on the identification of specific bacterial communities by microfloraDNA (mfDNA) amplification. A multiplex real time-PCR assay (ForFLUID kit) has been developed for identifying biological fluids and for discrimination among vaginal, oral and fecal samples. In order to test its efficacy and reliability of the assay in the identification of vaginal fluids, an interlaboratory evaluation has been performed on homogeneous vaginal swabs. All the involved laboratories were able to correctly recognize all the vaginal swabs, and no false positives were identified when the assay was applied on non-vaginal samples. The assay represents an useful molecular tool that can be easily adopted by forensic geneticists involved in vaginal fluid identification.
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http://dx.doi.org/10.1016/j.jflm.2013.10.016DOI Listing
January 2014

A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population.

Forensic Sci Int Genet 2014 Jan 17;8(1):101-8. Epub 2013 Aug 17.

Department of Forensic Sciences, The George Washington University, Washington, DC, United States. Electronic address:

When an STR DNA profile obtained from crime scene evidence does not match identified suspects or profiles from available databases, further DNA analyses targeted at inferring the possible ancestral origin and phenotypic characteristics of the perpetrator could yield valuable information. Single Nucleotide Polymorphisms (SNPs), the most common form of genetic polymorphisms, have alleles associated with specific populations and/or correlated to physical characteristics. We have used single base primer extension (SBE) technology to develop a 50 SNP assay (composed of three multiplexes) designed to predict ancestry among the primary U.S. populations (African American, East Asian, European American, and Hispanic American/Native American), as well as pigmentation phenotype (eye, hair, and skin color) among European American. We have optimized this assay to a sensitivity level comparable to current forensic DNA analyses, and shown robust performance on forensic-type samples. In addition, we developed a prediction model for ancestry in the U.S. population, based on the random match probability and likelihood ratio formulas already used in forensic laboratories. Lastly, we evaluated the biogeographic ancestry prediction model using a test set, and we evaluated an existing model for eye color with our U.S. sample set. Using these models with recommended thresholds, the 50 SNP assay provided accurate ancestry information in 98.6% of the test set samples, and provided accurate eye color information in 61% of the European samples tested (25% were inconclusive and 14% were incorrect). This method, which uses equipment already available in forensic DNA laboratories, is recommended for use in U.S. forensic casework to provide additional information about the donor of a DNA sample when the STR profile has not been linked to an individual.
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http://dx.doi.org/10.1016/j.fsigen.2013.07.010DOI Listing
January 2014

SNP genotyping using multiplex single base primer extension assays.

Methods Mol Biol 2009 ;578:379-91

Department of Forensic Sciences, The George Washington University, Washington, DC, USA.

Single nucleotide polymorphisms (SNPs) are the most common form of polymorphisms present in the human genome. The single base primer extension (SBE) method is an effective and sensitive tool that can type over 30 known loci scattered throughout an organism's genome in a single reaction. It allows the typing of tetra-allelic SNPs and has been adapted to a broad range of analytical necessities: single-cell analysis, molecular diagnosis of monogenic diseases, forensic mitochondrial DNA analysis on highly degraded human remains, and high-throughput SNP screening for population studies. Every SBE-based assay will need customized optimization efforts that are generally proportional to the number of desired SNPs typed in a single reaction. This chapter offers a detailed outline on which to base the design and optimization of any multiplex SBE assay that can then be tailored to the analytical conditions that characterize each specific application.
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http://dx.doi.org/10.1007/978-1-60327-411-1_23DOI Listing
December 2009

Development of a multiplex single base extension assay for mitochondrial DNA haplogroup typing.

Croat Med J 2007 Aug;48(4):460-72

The George Washington University Department of Forensic Sciences, Washington, DC, USA.

Aim: To provide a screening tool to reduce time and sample consumption when attempting mitochondrial DNA (mtDNA) haplogroup typing.

Methods: A single base primer extension assay was developed to enable typing, in a single reaction, of twelve mtDNA haplogroup specific polymorphisms. For validation purposes a total of 147 samples were tested including 73 samples successfully haplogroup typed using mtDNA control region (CR) sequence data, 20 samples inconclusively haplogroup typed by CR sequence data, 21 samples previously haplogroup typed using RFLP analysis, and 31 samples of known ancestral origin without previous haplogroup typing. Additionally, two highly degraded human bones embalmed and buried in the early 1950s were analyzed using the SNP multiplex.

Results: When the SNP multiplex was used to type the 96 previously CR sequenced specimens, an increase in haplogroup or macrohaplogroup assignment relative to conventional CR sequence analysis was observed. The single base extension assay was also successfully used to assign a haplogroup to decades-old, embalmed skeletal remains dating to World War II.

Conclusion: The SNP multiplex was successfully used to obtain haplogroup status of highly degraded human bones, and demonstrated the ability to eliminate possible contributors. The SNP multiplex provides a low-cost, high throughput method for typing of mtDNA haplogroups A, B, C, D, E, F, G, H, L1/L2, L3, M, and N that could be useful for screening purposes for human identification efforts and anthropological studies.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2080571PMC
August 2007

Validation of a large Italian Database of 15 STR loci.

Forensic Sci Int 2006 Jan 22;156(2-3):266-8. Epub 2005 Apr 22.

Center of Statistical Genetics, SS Abetone e Brennero 2, 56127 Pisa, Italy.

Results from a collaborative exercise with proficiency testing conducted by 20 Italian laboratories on the 15 loci included in the Identifiler kit were analyzed by allele sharing methods and by standard population genetics tests. The validated database, including about 1500 subjects, was merged with that of a previous exercise conducted on nine loci, and the resulting allele frequencies, subdivided by Italian region, were published on-line.
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http://dx.doi.org/10.1016/j.forsciint.2005.03.001DOI Listing
January 2006

Short tandem repeats haplotyping of the HLA region in preimplantation HLA matching.

Eur J Hum Genet 2005 Aug;13(8):953-8

EmbryoGen - Center for Preimplantation Genetic Diagnosis, Rome, Italy.

Recently, preimplantation genetic diagnosis (PGD) has been considered for several indications beyond its original purpose, not only to test embryos for genetic disease but also to select embryos for a nondisease trait, such as specific human leukocyte antigen (HLA) genotypes, related to immune compatibility with an existing affected child in need of a haematopoetic stem cell (HSC) transplant. We have optimized an indirect single-cell HLA typing protocol based on a multiplex fluorescent polymerase chain reaction (PCR) of short tandem repeat (STR) markers scattered throughout the HLA complex. The assay was clinically applied in 60 cycles from 45 couples. A conclusive HLA-matching diagnosis was achieved in 483/530 (91.1%) of the embryos tested. In total, 74 (15.3%) embryos revealed an HLA match with the affected siblings, 55 (11.4%) of which resulted unaffected and 46 (9.5%) have been transferred to the patients. Nine pregnancies were achieved, five healthy HLA-matched children have already been delivered and cord blood HSCs, were transplanted to three affected siblings, resulting in a successful haematopoietic reconstruction.
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http://dx.doi.org/10.1038/sj.ejhg.5201435DOI Listing
August 2005