Alessandra Carnevale

The genetics of Mexico recapitulates Native American substructure and affects biomedical traits

The population structure of Native Mexicans The genetics of indigenous Mexicans exhibit substantial geographical structure, some as divergent from each other as are existing populations of Europeans and Asians. By performing genome-wide analyses on Native Mexicans from differing populations, Moreno-Estrada et al. successfully recapitulated the pre-Columbian substructure of Mexico. This ancestral structure is evident among cosmopolitan Mexicans and is correlated with subcontinental origins and medically relevant aspects of lung function. These findings exemplify the importance of understanding the genetic contributions of admixed individuals. Science, this issue p. 1280 Indigenous and cosmopolitan Mexican populations are highly structured with genetic variation of medical relevance. Mexico harbors great cultural and ethnic diversity, yet fine-scale patterns of human genome-wide variation from this region remain largely uncharacterized. We studied genomic variation within Mexico from over 1000 individuals representing 20 indigenous and 11 mestizo populations. We found striking genetic stratification among indigenous populations within Mexico at varying degrees of geographic isolation. Some groups were as differentiated as Europeans are from East Asians. Pre-Columbian genetic substructure is recapitulated in the indigenous ancestry of admixed mestizo individuals across the country. Furthermore, two independently phenotyped cohorts of Mexicans and Mexican Americans showed a significant association between subcontinental ancestry and lung function. Thus, accounting for fine-scale ancestry patterns is critical for medical and population genetic studies within Mexico, in Mexican-descent populations, and likely in many other populations worldwide.

Microtia: A Clinical and Genetic Study at the National Institute of Pediatrics in Mexico City

BACKGROUND Microtia is a malformation of the ear with extreme variability of expression. It is generally seen as an isolated malformation. However, some authors consider it to be a minimal manifestation of the oculo-auriculo-vertebral spectrum (OAVS), where, in addition, there are facial, vertebral, and renal abnormalities, among others. METHODS A total of 145 pediatric patients with unilateral or bilateral microtia not considered as part of a syndrome were studied. All patients were subjected to an intentional clinical examination, a familial history, and radiographic imaging studies for ruling out associated malformations. Patients were classified into two groups: group 1 (60%), with isolated microtia; and group 2 (40%), considered as OAVS, with microtia associated with hemifacial skeletal microsomia, vertebral and/or renal malformations. RESULTS No significant differences were found between the groups when the following variables were compared: gender; presence of unilateral or bilateral microtia; atretic external auditory canal; presence of preauricular tags; hearing loss of any type, and affection of the seventh cranial nerve, as well as associated malformations of other organs or systems. There were significant differences in relation to the presence of soft-tissue hemifacial microsomia, more frequently seen in patients with OAVS, because the majority of these patients had bone microsomia. Over 66% of the cases were sporadic and the rest were familiar. In 28.3% of the cases, the history suggested an autosomal-dominant inheritance pattern, and in 5.5%, an autosomal-recessive inheritance pattern, although in some familial cases, multifactorial inheritance could not be ignored. Some members in several families had isolated microtia, and others had mild characteristic manifestations of OAVS. CONCLUSIONS Our results support the hypothesis that isolated microtia is a minimal expression of OAVS. Therefore, it is recommended that patients with microtia be subjected to intentional studies that search for malformations and physical examinations of first-degree relatives for adequate genetic counseling and management.

Association of the genetic marker for abacavir hypersensitivity HLA-B*5701 with HCP5 rs2395029 in Mexican Mestizos

UNLABELLED Prospective screening for HLA-B*5701 decreases or abolishes abacavir hypersensitivity reaction. In Caucasians, the HLA complex protein 5 gene (HCP5) rs2395029(G) allele is in complete linkage disequilibrium (LD) with HLA-B*5701 (r(2) = 1). AIM To assess the frequency of HLA-B*5701 and its LD with HCP5 rs2395029(G) allele, to extend our knowledge of genetic variants that are of critical relevance for the development of pharmacogenetics in Mexico. MATERIALS & METHODS We genotyped 300 Mexican Mestizos from the Mexican Genome Diversity Project. HLA-B*5701 genotyping was performed using a DNA sequencing method. HCP5 rs2395029 was genotyped using a custom TaqMan(®) SNP genotyping assay and confirmed by direct sequencing. Genotypes for 14 SNPs in the HCP5 region were retrieved from the Mexican Genome Diversity Project database for LD analysis. RESULTS HLA-B*5701 carrier frequency was 2% and the allelic frequency was 0.010. Haplotype analysis revealed that HLA-B*5701 and the HCP5 rs2395029(G) allele are in complete LD (r(2) = 1) in this Mexican Mestizos sample. CONCLUSION It is feasible to have a pharmacogenetic program based on HCP5 rs2395029 genotyping as a screening tool with confirmation of HLA-B*5701 carriage by sequenciation, to prevent abacavir hypersensitivity reaction in Mexican patients before initiating abacavir therapy.

Effect of hydroxyurea and normal plasma on DNA synthesis in lymphocytes from Fanconi anemia patients.

Fanconi anemia (FA) is characterized at the cellular level by a high frequency of spontaneous chromosomal aberrations; crosslinking agents cause an abnormal increase in the frequency of chromosomal damage, and semiconservative DNA synthesis is severely inhibited. Deoxyribonucleotides are needed in both semiconservative and repair DNA synthesis. To investigate the involvement of deoxyribonucleotide pools in the inhibition of DNA synthesis in FA, we evaluated the effect on FA lymphocytes of hydroxyurea (HU), an inhibitor of ribonucleotide reductase which is known to alter the intracellular levels of deoxyribonucleotides. To achieve this goal, lymphocyte cultures of 4 FA patients and 4 normal individuals were used. Cultures were treated with HU and/or mitomycin C and normal human plasma. All cultures were processed to detect the number of DNA synthesizing nuclei by autoradiography. Scoring of 2000 nuclei for each kind of culture every 6 h in the last 24 h of incubation showed that, in long incubation periods, DNA synthesis in FA is largely inhibited by HU and this hypersensitivity may be partially decreased by addition of normal human plasma. It is known that recovery from damage induced by HU involves several enzymes such as flavin oxido-reductase, superoxide dismutase and catalase which are involved in the production or scavenging of O2 radicals; FA cells are deficient in the detoxification of oxygen and this could explain the response of FA cells to HU.

Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing

Understanding the genetic structure of Native American populations is important to clarify their diversity, demographic history, and to identify genetic factors relevant for biomedical traits. Here, we show a demographic history reconstruction from 12 Native American whole genomes belonging to six distinct ethnic groups representing the three main described genetic clusters of Mexico (Northern, Southern, and Maya). Effective population size estimates of all Native American groups remained below 2,000 individuals for up to 10,000 years ago. The proportion of missense variants predicted as damaging is higher for undescribed (~ 30%) than for previously reported variants (~ 15%). Several variants previously associated with biological traits are highly frequent in the Native American genomes. These findings suggest that the demographic and adaptive processes that occurred in these groups shaped their genetic architecture and could have implications in biological processes of the Native Americans and Mestizos of today.People of Mexico have diverse historical and genetic background. Here, Romero-Hidalgo and colleagues sequence whole genomes of Native Americans of Mexico, and show demographic history and genetic variation shared among subgroups of Native Americans.

Patient follow-up is a major problem at genetics clinics

Children with genetic diseases must be followed for long periods of time to seek new findings. Other patients require further check‐ups and studies to be diagnosed. Some patients never return for medical care after the first consultation, which may have serious consequences. We reviewed 400 medical charts of patients with genetic disease to analyze overall attendance to the genetics clinic, investigate some of the causes of failure to seek medical advice, and determine the differences between those first seen as outpatients or as inpatients. The mean follow‐up period was 8.3 months (range 0–79), and the average number of visits was 2.8 (range 1–16). Forty eight percent of the cases first seen as inpatients were evaluated only once and 14% twice; while 22 and 21% of the 300 cases first seen as outpatients attended once and twice, respectively (P = 0.0). Appointment keeping was apparently not affected by the presence or absence of diagnosis. Overall, 97 patients were discharged, 7 died, 55 continued on follow‐up, 62 attended other hospital services—but not genetics—and 179 were completely lost to follow‐up. Diagnosed patients were counseled more frequently than undiagnosed patients (62 vs. 5%); and 71% of the diagnosed patients first seen as outpatients but only 36% of undiagnosed cases first seen as inpatients were counseled, differences between these two groups were significant (P = 0.005). We conclude that keeping the patient with genetic disease on follow‐up is a difficult task. New educational strategies must be planned to improve this worrisome situation.

In Mexican Mestizos the HCP5 rs2395029 SNP may be a genetic marker for screening abacavir hypersensitivity

A letter in response to: Badulli C, Sestini R, Sbarsi I et al. Tag SNPs of the ancestral haplotype 57.1 do not substitute HLA-B*57:01 typing for eligibility to abacavir treatment in the Italian population. Pharmacogenomics 13(3), 247–249 (2012).