Biomedical subjects

Claudio M Bravi

Publications and source records attributed to Claudio M Bravi.

8 recordsLinked to original sources

PubMed2006

High penetrance of sequencing errors and interpretative shortcomings in mtDNA sequence analysis of LHON patients.

For identifying mutation(s) that are potentially pathogenic it is essential to determine the entire mitochondrial DNA (mtDNA) sequences from patients suffering from a particular mitochondrial disease, such as Leber hereditary optic neuropathy (LHON). However, such sequencing efforts can, in the worst case, be riddled with errors by imposing phantom mutations or misreporting variant nucleotides, and moreover, by inadvertently regarding some mutations as novel and pathogenic, which are actually known to define minor haplogroups. Under such circumstances it remains unclear whether the disease-associated mutations would have been determined adequately. Here, we re-analyse four problematic LHON studies and propose guidelines by which some of the pitfalls could be avoided.

Artifacts↗

PubMed2006

What is a 'novel' mtDNA mutation--and does 'novelty' really matter?

The hunt for pathogenic mitochondrial DNA (mtDNA) mutations is often fueled by the seeming novelty of mutations that are either nonsynonymous or affect the protein synthesis machinery in patients. In order to determine the novelty of a detected mutation, the working geneticist nearly always consults MITOMAP--often exclusively. By reanalyzing some case studies of refractory anemia with ring sideroblasts, prostate cancer, and hearing impairment, we demonstrate that the practice of solely relying on MITOMAP can be most misleading. A notorious example is the T1243C mutation, which was assessed to be novel and deemed to be associated with some (rare) disease simply because researchers did not realize that T1243C defines a deep branch in the Eurasian mtDNA phylogeny. The majority of 'novel' mutations suspected of being pathogenic are in actual fact known (and presumably neutral) polymorphisms (although unknown to MITOMAP), and this becomes glaringly evident when proper database searches and straightforward Internet queries are carried out.

Anemia, Refractory, with Excess of Blasts↗

PubMed2006

A reappraisal of complete mtDNA variation in East Asian families with hearing impairment.

In a number of recent studies, we summarized the obvious errors and shortcomings that can be spotted in many (if not most) mitochondrial DNA (mtDNA) data sets published in medical genetics. We have reanalyzed here the complete mtDNA genome data published in various recent reports of East Asian families with hearing impairment, using a phylogenetic approach, in order to demonstrate the persistence of lab-specific mistakes in mtDNA genome sequencing in cases where those caveats were (deliberately) neglected. A phylogenetic reappraisal of complete mtDNAs with mutation A1555G (or G11778A) indeed supports the suggested lack of association between haplogroup background and phenotypic presentation of these mutations in East Asians. In contrast, the claimed pathogenicity of mutation T1095C in Chinese families with hearing impairment seems unsupported, basically because this mutation is rather basal in the mtDNA phylogeny, being specific to haplogroup M11 in East Asia. The roles of other haplogroup specific or associated variants, such as A827G, T961C, T1005C, in East Asian subjects with aminoglycoside-induced and non-syndromic hearing loss are also unclear in view of the known mtDNA phylogeny.

DNA, Mitochondrial↗

PubMed2006

A revertant of the major founder Native American haplogroup C common in populations from northern South America.

We examined the mtDNA RFLP diversity of 17 Native American populations from Colombia. Five of the populations studied were found to have variable frequencies of a mtDNA type lacking the characteristic changes of haplogroups A-D. Sequencing of mtDNA HVS-I and II showed that this "null" RFLP type carries all the substitutions characteristic of Native American founder lineage C. A back mutation has therefore recreated the +13,259 HincII/-13,262 AluI restriction sites that tipify RFLP haplogroup C. This revertant C lineage is further characterized by three changes in HVS-II sequence: C/T transitions at positions 115 and 152, and the deletion of an A residue at position 116. This lineage is observed at high frequency mostly in populations from Greenberg's Equatorial-Tucano linguistic family. Genetic structure analyses are consistent with the reversion mutation occurring at an early stage during the tribalization process.

Colombia↗

PubMed2005

Phantom mutation hotspots in human mitochondrial DNA.

Phantom mutations are systematic artifacts generated in the course of the sequencing process. Contra common belief these artificial mutations are nearly ubiquitous in sequencing results, albeit at frequencies that may vary dramatically. The amount of artifacts depends not only on the sort of automated sequencer and sequencing chemistry employed, but also on other lab-specific factors. An experimental study executed on four samples under various combinations of sequencing conditions revealed a number of phantom mutations occurring at the same sites of mitochondrial DNA (mtDNA) repeatedly. To confirm these and identify further hotspots for artifacts, > 5000 mtDNA electropherograms were screened for artificial patterns. Further, > 30 000 published hypervariable segment I sequences were compared at potential hotspots for phantom mutations, especially for variation at positions 16085 and 16197. Resequencing of several samples confirmed the artificial nature of these and other polymorphisms in the original publications. Single-strand sequencing, as typically executed in medical and anthropological studies, is thus highly vulnerable to this kind of artifacts. In particular, phantom mutation hotspots could easily lead to misidentification of somatic mutations and to misinterpretations in all kinds of clinical mtDNA studies.

Artifacts↗

PubMed2004

A call for mtDNA data quality control in forensic science.

There is increasing evidence that many of the mitochondrial DNA (mtDNA) databases published in the fields of forensic science and molecular anthropology are flawed. An a posteriori phylogenetic analysis of the sequences could help to eliminate most of the errors and thus greatly improve data quality. However, previously published caveats and recommendations along these lines were not yet picked up by all researchers. Here we call for stringent quality control of mtDNA data by haplogroup-directed database comparisons. We take some problematic databases of East Asian mtDNAs, published in the Journal of Forensic Sciences and Forensic Science International, as examples to demonstrate the process of pinpointing obvious errors. Our results show that data sets are not only notoriously plagued by base shifts and artificial recombination but also by lab-specific phantom mutations, especially in the second hypervariable region (HVR-II).

DNA Fingerprinting↗

PubMed2004

A simple method for domestic animal identification in Argentina using PCR-RFLP analysis of cytochrome b gene.

We developed a simple, quick assay in order to discriminate forensic samples among human, and common domestic and livestock species of the Pampean region, Argentina. A mitochondrial cytochrome b fragment amplified with universal primers was separately digested with three restriction enzymes (AluI, HaeIII, and HinfI) and the resulting fragments were resolved through electrophoresis in polyacrylamide gels. This PCR-RFLP method allowed us to identify the target species and worked on degraded samples. The assay was successfully applied in livestock robbery cases in Argentine, and may be useful when attempting a first assessment as to the specific status of a forensic evidence.

Animals↗

PubMed2002

East Asian genotypes of Helicobacter pylori strains in Amerindians provide evidence for its ancient human carriage.

Phylogenies of indigenous microbes have been used as surrogates for the origins of the hosts that carry them. Conversely, polymorphisms may be used to date the spread of a microbial species when information about their host populations is available. Therefore, we examined polymorphisms in Helicobacter pylori, which persistently colonize the human stomach, to test the hypothesis that they have been ancient inhabitants of humans. Three H. pylori loci that previously have been shown to have phylogeographic affinity have been analyzed for two populations with different ethnic origins from Venezuela. In a group of Amerindian subjects from Amazonia, East Asian H. pylori genotypes were present for each of the loci examined but were absent in a mestizo population from Caracas. These findings provide evidence that H. pylori has been present in humans at least since ancestors of Amerindians migrated from Asia more than 11,000 years ago.

Africa South of the Sahara↗