Papers by Cinzia Battaggia
PubMed, Dec 22, 2021
In recent decades, the scientific community has become aware of the importance of science being e... more In recent decades, the scientific community has become aware of the importance of science being effectively open in order to speed up scientific and technological progress. In this context, the achievement of a robust, effective and responsible form of data sharing is now widely acknowledged as a fundamental part of the research process. The production and resolution of human genomic data has steadily increased in recent years, mainly due to technological advances and decreasing costs of DNA genotyping and sequencing. There is, however, a downside to this process due to the huge increase in the complexity of the data and related metadata. This means it is advisable to go beyond traditional forms of sharing analysis, which have focused on data availability only. Here we present a pilot study that aims to complement a survey on the availability of data related to peer-reviewed publications with an analysis of their findability, accessibility, useability and assessability (according to the "intelligent data openness" scheme). Sharing rates in genomic anthropology (73.0%) were found to be higher than human genomics (32.4%), but lower than closely related research fields (from 96.8% to 79.2% for paleogenetics and evolutionary genetics, respectively). We discuss the privacy and methodological issues that could be linked to this finding. Comparisons of sharing rates across a wide range of disciplines has suggested that the idea of human genomics as a forerunner for the open data movement should be questioned. Finally, both in genomic anthropology and human genomics, findability and useability were found to be compliant with the expectations of an intelligent data openness, whereas only a minor part of studies met the need to make the data completely assessable.
Scientific Reports, 2016
The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Al... more The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps – putatively in genetic continuity with the Tyrolean Iceman—and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000...
PloS one, 2015
This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphis... more This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving v...
This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphis... more This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6 % ± 2.1%) and substan-tially higher than observed in other fields of genetic research (evolutionary, medical and fo-rensic genetics). Both a questionnaire-based survey and the examination of Journals’ editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three impor-tant aspects. First, our results imply that researchers ’ awareness of the importance of open-ness and transparency for scientific progress may complement stakeholders ’ policies in achieving very h...
A number of studies carried out since the early ‘70s has investigated the effects of isolation on... more A number of studies carried out since the early ‘70s has investigated the effects of isolation on genetic variation within and among human populations in diverse geographical contexts. However, no extensive analysis has been carried out on the heterogeneity among genomes within isolated populations. This issue is worth exploring since events of recent admixture and/or subdivision could potentially disrupt the genetic homogeneity which is to be expected when isolation is prolonged and constant over time. Here, we analyze literature data relative to 87,818 autosomal single-nucleotide polymorphisms, which were obtained from a total of 28 European populations. Our results challenge the traditional paradigm of population isolates as genetically (and genomically) uniform entities. In fact, focusing on the distribution of variance of intra-population diversity measures across individuals, we show that the inter-individual heterogeneity of isolated populations is at least comparable to the ...
Scientific reports, Feb 1, 2017
Human populations are often dichotomized into "isolated" and "open" categorie... more Human populations are often dichotomized into "isolated" and "open" categories using cultural and/or geographical barriers to gene flow as differential criteria. Although widespread, the use of these alternative categories could obscure further heterogeneity due to inter-population differences in effective size, growth rate, and timing or amount of gene flow. We compared intra and inter-population variation measures combining novel and literature data relative to 87,818 autosomal SNPs in 14 open populations and 10 geographic and/or linguistic European isolates. Patterns of intra-population diversity were found to vary considerably more among isolates, probably due to differential levels of drift and inbreeding. The relatively large effective size estimated for some population isolates challenges the generalized view that they originate from small founding groups. Principal component scores based on measures of intra-population variation of isolated and open popul...
The advent of the digital era is radically changing ���������������������������������������������... more The advent of the digital era is radically changing ���������������������������������������������������� disseminated. However, to what extent this ongoing revolution might foster the advancement of science depends on our ability to make information availa-�������������������������������������������������������� last two decades that the importance of a robust, effective and sustainable data sharing has been fully
PLoS ONE, 2013
Great European mountain ranges have acted as barriers to gene flow for resident populations since... more Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups,
Anthropologischer Anzeiger
Within the frame of an anthropobiological survey on some populations of Cameroon (1985-1991), Hb ... more Within the frame of an anthropobiological survey on some populations of Cameroon (1985-1991), Hb beta data were collected from numerous ethnic groups including Bakaka, Bamileke, Daba, Fali, Guiziga, Kanuri, Mada, Mafa, Mundang, Uldeme, Podokwo, Tali, Tupuri, Fulbe, Mandara, Ewondo and Bassa. Hb beta *S allele frequencies ranged from 0.008 +/- 0.003 (among Fali) to 0.152 +/- 0.020 (among Mandara) and 0.152 +/- 0.044 (among Podokwo), whereas Hb beta *S was found to be absent among Tupuri. Hb beta *C was observed among Bamileke (0.001 +/- 0.001), Fali (0.003 +/- 0.002), Fulbe (0.002 +/- 0.002), Mafa (0.005 +/- 0.005), Mundang (0.005 +/- 0.005), Tupuri (0.010 +/- 0.007) and Podokwo (0.015 +/- 0.015). The possible reasons for these variations in allele frequencies are discussed.
Human Biology
We recently proposed a biochemical model of genetic resistance to falciparum malaria based on the... more We recently proposed a biochemical model of genetic resistance to falciparum malaria based on the role of oxidant stress (of parasitic origin) in inducing the irreversible oxidation of hemoglobin and its binding to the erythrocyte membrane (Destro-Bisol et al. 1996). To test the model, we analyzed the relationships between the polymorphisms at the hemoglobin beta chain (HBB) and red cell glutathione peroxidase (GPX1) loci in 18 populations that had been subjected to endemic malaria (Cameroon and Central African Republic). The erythrocytes of GPX1*2 heterozygotes should be more efficient in sheltering the cell membrane from irreversible oxidation and binding of hemoglobin caused by the oxidant stress exerted by Plasmodium falciparum. According to our model, the GPX1*2 allele has an epistatic effect on the HBB*A/*S genotype by lowering its protection against falciparum malaria. In turn, this should decrease the fitness of the HBB*A/*S-GPX1*2/*1 genotype. Our predictions were confirmed...
Journal of Forensic Sciences
Anthropologischer Anzeiger
Microfilter absorbed whole blood samples from 223 Tanzanian babies and 189 adults from Cameroon h... more Microfilter absorbed whole blood samples from 223 Tanzanian babies and 189 adults from Cameroon have been examined. Blood specimens are difficult to obtain from African suburban and rural areas, and lack of storage and transportation facilities can prevent the collection of samples. We evaluated some microassays employing whole blood collected on filter paper. This method is a well established technique in neonatal screening for endocrinometabolic diseases. We also developed microassays for whole dried blood spots to type AB0 blood groups and HIV disease using commercial reagents. Phenotype and gene frequencies for AB0 and hemoglobin systems as well as our results concerning the typings of thyroxine (T4), thyroid stimulating hormone (TSH), human immunodeficiency virus (HIV) and hepatitis B virus (HBV) are reported.
PloS one, 2015
This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphis... more This study analyzes data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on ancient human DNA published between 1988 and 2013. The estimated sharing rate was not far from totality (97.6% ± 2.1%) and substantially higher than observed in other fields of genetic research (evolutionary, medical and forensic genetics). Both a questionnaire-based survey and the examination of Journals' editorial policies suggest that this high sharing rate cannot be simply explained by the need to comply with stakeholders requests. Most data were made available through body text, but the use of primary databases increased in coincidence with the introduction of complete mitochondrial and next-generation sequencing methods. Our study highlights three important aspects. First, our results imply that researchers' awareness of the importance of openness and transparency for scientific progress may complement stakeholders' policies in achieving v...
Clinical chemistry, 1992
Technical Briefs (-300 words text) summarize findings that are of interest to a relatively limite... more Technical Briefs (-300 words text) summarize findings that are of interest to a relatively limited audience. Readers desiring fuller details may obtain them by writing directly to the author(s). Briefs dealing with procedure or instrumentation intercomparisons, evaluations, or improvements (including kit applications) should be sent to Clinical Chemistry News, 2029 K Street, Washington, DC 20006. Thn. after stait of Power settings mln 700 V, 2 W, unlimitedmA 592
The advent of the digital era is radically changing ���������������������������������������������... more The advent of the digital era is radically changing ���������������������������������������������������� disseminated. However, to what extent this ongoing revolution might foster the advancement of science depends on our ability to make information availa-�������������������������������������������������������� last two decades that the importance of a robust, effective and sustainable data sharing has been fully
Journal of anthropological sciences = Rivista di antropologia : JASS / Istituto italiano di antropologia, 2014
The animal and plant biodiversity of the Italian territory is known to be one of the richest in t... more The animal and plant biodiversity of the Italian territory is known to be one of the richest in the Mediterranean basin and Europe as a whole, but does the genetic diversity of extant human populations show a comparable pattern? According to a number of studies, the genetic structure of Italian populations retains the signatures of complex peopling processes which took place from the Paleolithic to modern era. Although the observed patterns highlight a remarkable degree of genetic heterogeneity, they do not, however, take into account an important source of variation. In fact, Italy is home to numerous ethnolinguistic minorities which have yet to be studied systematically. Due to their difference in geographical origin and demographic history, such groups not only signal the cultural and social diversity of our country, but they are also potential contributors to its bio-anthropological heterogeneity. To fill this gap, research groups from four Italian Universities (Bologna, Cagliar...
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Papers by Cinzia Battaggia