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Gianmarco FERRI

Personale tecnico amministrativo
Dipartimento di Scienze Biomediche, Metaboliche e Neuroscienze sede Policlinico

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Pubblicazioni

2015 - Forensic botany II, DNA barcode for land plants: Which markers after the international agreement? [Articolo su rivista]
Ferri, Gianmarco; Corradini, Beatrice; Ferrari, Francesca; Santunione, Anna Laura; Palazzoli, Federica; Alu', M. 2.
abstract

The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for forensic botany. Based on obtained results, we recommend the adoption of a two-locus combination with rbcL+trnH-psbA plastid markers, which currently best satisfies forensic needs for botanical species identification.

2012 - Development of six-SNPs assay for forensic analysis in European population [Abstract in Atti di Convegno]
Ferri, Gianmarco; Ferrari, F.; Corradini, B.; Santunione, Anna Laura; Alu', Milena
abstract

Y-chromosomal SNPs analysis show regional specificity useful in forensic investigation for inferring the male genetic background of individuals and population and to predict biogeographical origin of the donor of a crime scene sample. Due to its exclusively paternal inheritance, the Y-chromosome has been extensively used in evolutionary and forensic genetics to investigate the phylogeny and the history of population and their migration. A large scale parsimonious phylogenetic tree representing worldwide Y-chromosome variation has been constructed and comprises major haplogroups. The aim of this study was to set-up six multiplex assays based on SNaPshot kit to identify markers inside major clades of European population. Specifically, we design PCR and minisequencing primers targeting a total of 33 Y-mutations downstream R1*, I*, J2*, G* and E1b1b1* haplogroups. The PCR fragments were chosen to get the shortest product possible in order to improve the performance in degraded samples (amplicons principally ranging from 56 bp to 140 bp). This assay based on a 6-multiplex PCR reaction is a suitable tool for detecting the main European haplogroups in forensic casework and population study.

2010 - Y-STR variation in Albanian populations: implications on the match probabilities and the genetic legacy of the minority claiming an Egyptian descent. [Articolo su rivista]
Ferri, Gianmarco; Tofanelli, S; Alù, M; Taglioli, L; Radheshi, Erjon; Corradini, Beatrice; Paoli, G; Capelli, C; Beduschi, Giovanni
abstract

Y chromosome variation at 12 STR (the Powerplex(R) Y system core set) and 18 binary markers was investigated in two major (the Ghegs and the Tosks) and two minor (the Gabels and the Jevgs) populations from Albania (Southern Balkans). The large proportion of haplotypes shared within and between groups makes the Powerplex 12-locus set inadequate to ensure a suitable power of discrimination for the forensic practice. At least 85% of Y lineages in the Jevgs, the cultural minority claiming an Egyptian descent, turned out to be of either Roma or Balkan ancestry. They also showed unequivocal signs of a common genetic history with the Gabels, the other Albanian minority practising social and cultural Roma traditions.

2009 - Forensic botany: species identification of botanical trace evidence using a multigene barcoding approach [Articolo su rivista]
Ferri, Gianmarco; Alù, M; Corradini, Beatrice; Beduschi, Giovanni
abstract

Forensic botany can provide significant supporting evidence during criminal investigations. However, it is still an underutilized field of investigation with its most common application limited to identifying specific as well as suspected illegal plants. The ubiquitous presence of plant species can be useful in forensics, but the absence of an accurate identification system remains the major obstacle to the present inability to routinely and correctly identify trace botanical evidence. Many plant materials cannot be identified and differentiated to the species level by traditional morphological characteristics when botanical specimens are degraded and lack physical features. By taking advantage of a universal barcode system, DNA sequencing, and other biomolecular techniques used routinely in forensic investigations, two chloroplast DNA regions were evaluated for their use as "barcoding" markers for plant identification in the field of forensics. We therefore investigated the forensic use of two non-coding plastid regions, psbA-trnH and trnL-trnF, to create a multimarker system for species identification that could be useful throughout the plant kingdom. The sequences from 63 plants belonging to our local flora were submitted and registered on the GenBank database. Sequence comparison to set up the level of identification (species, genus, or family) through Blast algorithms allowed us to assess the suitability of this method. The results confirmed the effectiveness of our botanic universal multimarker assay in forensic investigations.

2009 - Slow and fast evolving markers typing in Modena males (North Italy) [Articolo su rivista]
Ferri, Gianmarco; Alu', Milena; Corradini, Beatrice; Radheshi, Erjon; Beduschi, Giovanni
abstract

One hundred thirty male individuals, strictly selected for their geographical origin and for typical regional surnames were submitted to the analysis. 17 STRs (short tandem repeats) loci and 19 SNPs binary markers (single nucleotide polymorphisms) of male-specific region of the Y chromosome (MSY) were typed to well characterize the selected population of Modena province. The availability of joint distribution of MSY haplotypes and haplogroup frequencies is becoming an important tool for both human evolutionary studies and forensic investigation, but large databases of complete Y-lineages are needed for a better understanding of the power of the combined use of Y-specific polymorphisms. A total of 129 haplotypes and 9 haplogroups were found and R1b haplogroup with a frequency of 67.7% was the most frequent, as expected because of the geographical location of the sample (Northwestern Italy). The Modena Y-lineages (STRs and SNPs independently) were also compared with published data of other neighbouring populations' samples.

2009 - Species Identification Through DNA "Barcodes'' [Articolo su rivista]
Ferri, Gianmarco; Alù, M; Corradini, Beatrice; Licata, Manuela; Beduschi, Giovanni
abstract

Conventional methods for forensic species identification are mainly based on immunological procedures, which have limited applications for old and degraded specimens. The mitochondrial cytochrome b gene sequence has emerged in forensics among molecular methods. Recent investigations in the taxonomic field have suggested that a DNA-based identification system may aid the resolution of animal diversity and classification using sequence analysis and phylogenetic links. Selected gene sequences can be viewed as a genetic "barcode," which is enclosed in every cell, and barcoding is a standardized approach for characterizing species using short DNA sequences as a diagnostic biomarker for organisms. The aim of this study was to evaluate the potential of barcode mitochondrial genes, such as the cytochrome c oxidase sub 1 (COI) and the 16S rRNA gene, as a forensic tool. We developed a new approach for species testing and identification with a singleplex PCR amplification that will be useful not only in criminal casework but also in biosecurity, food authentication, investigation against poaching or illegal trade of endangered species, and wildlife enforcement. Seven fragments ranging from 157 to 541 bp (base pairs) in humans were selected from COI and 16S rRNA genes by different redesigned sets of primers suitable for forensic purposes. The specificity of each primer pair was evaluated with a single PCR reaction on different substrates, and the diversity values were calculated by statistical tests to select a set of markers that could be useful in different caseworks. A case example of forensic species identification is also presented.

2008 - Molecular characterisation and population genetics of the DYS458 .2 allelic variant. 22st [Articolo su rivista]
Ferri, Gianmarco; C., Robino; Alu', Milena; D., Luiselli; S., Tofanelli; L., Caciagli; V., Onofri; S., Pelotti; C., Di Gaetano; F., Crobu; Beduschi, Giovanni; C., Capelli
abstract

We recently found a number of intermediate DYS458 alleles, indicated as .2. This allelic variant is distributed in several populations, but currently no information is available regarding the molecular structure and the genealogical correlation of chromosomes with this variant. The molecular characterisation of such allele, its worldwide distribution and the correlated evolutionary history are the subject of the present paper. Molecular and genealogical data are suggestive of a single origin for the .2 variant. Phylogeographic analysis points to either a Middle East or East African origin, but additional data is necessary to clarify this point. Our results suggest that the .2 variants is a stable polymorphism and that it could be used for population studies.

2005 - Development of a heptaplex PCR system to analyse X-chromosome STR loci from five Italian population samples - A collaborative study [Articolo su rivista]
Bini, C; Ceccardi, S; Ferri, Gianmarco; Pelotti, S; Alu', Milena; Roncaglia, E; Beduschi, Giovanni; Caenazzo, L; Ponzano, E; Tasinato, P; Turchi, C; Buscemi, L; Mazzanti, Marta; Tagliabracci, A; Toni, C; Spinetti, I; Domenici, R; Presciuttini, S.
abstract

Many X-chromosome short tandem repeats (X-STRs) have been validated for forensic use even if further studies are needed on allele frequencies and mutation rates to evaluate the extent of polymorphism in different populations and to establish reference databases useful for forensic applications and for anthropological studies. A single multiplex reaction of seven X-STRs, which includes the DXS6789, HUMARA, DXS10011, DXS7423, HPRTB, DXS6807, DXS101 loci, is presented and their allele frequency distribution in a large population sample including 556 subjects (268 females and 288 males) analysed by five forensic laboratories of Central and Northern Italy is shown. Our results demonstrate the feasibility of a single amplification/detection reaction involving seven markers of the X chromosome, which can be fruitfully used in complex kinship analysis.