Secuenciación de genoma completo: un salto cualitativo en los estudios genéticos / Whole genome sequencing: a qualitative leap forward in genetic studies

Resumen. En estos momentos se encuentra en plena expansión la llamada secuenciación paralela o de siguiente generación -next generation sequencing (NGS)-, que establece un salto de varios órdenes de magnitud en la longitud de los fragmentos secuenciados y la rapidez de su secuenciación. La NGS permite la secuenciación de un genoma humano completo en el tiempo y el coste económico de secuenciar dos o tres genes grandes con la técnica de Sanger. Mediante la NGS se pasa de examinar genes específicos seleccionados mediante estudio del fenotipo a explorar genomas enteros de grupos humanos o de otras especies. Esto está permitiendo conocer no sólo cómo es un genoma individual, sino cómo cambia el genoma humano de persona a persona, cómo difieren los genomas entre diferentes grupos humanos, e incluso cómo difiere el genoma de un tumor respecto del genoma sano del huésped (AU)

Summary. At the present time the so-called parallel or next generation sequencing (NGS) technique is rapidly expanding and developing; this process establishes a jump by several orders of magnitude in the length of the fragments sequenced and the speed with which this sequencing is carried out. NGS allows a whole human genome to be sequenced in the same amount of time and with the same economic cost required to sequence two or three large genes using the Sanger technique. Use of NGS allows us to go from examining specific genes selected by studying the phenotype to exploring whole genomes of groups of humans or other species. This is making it possible to know not only what an individual genome is like but also how the human genome changes from one person to another, how genomes differ from one group of humans to another, and even how the genome differs in a tumour with respect to the healthy genome of the host (AU)

[Whole genome sequencing: a qualitative leap forward in genetic studies]. / Secuenciación de genoma completo: un salto cualitativo en los estudios genéticos.

At the present time the so-called parallel or next generation sequencing (NGS) technique is rapidly expanding and developing; this process establishes a jump by several orders of magnitude in the length of the fragments sequenced and the speed with which this sequencing is carried out. NGS allows a whole human genome to be sequenced in the same amount of time and with the same economic cost required to sequence two or three large genes using the Sanger technique. Use of NGS allows us to go from examining specific genes selected by studying the phenotype to exploring whole genomes of groups of humans or other species. This is making it possible to know not only what an individual genome is like but also how the human genome changes from one person to another, how genomes differ from one group of humans to another, and even how the genome differs in a tumour with respect to the healthy genome of the host.

Autosomal recessive Emery-Dreifuss muscular dystrophy caused by a novel mutation (R225Q) in the lamin A/C gene identified by exome sequencing.

INTRODUCTION: The aim of this study is to describe a new mutation in the LMNA gene diagnosed by whole exome sequencing. METHODS: A two-generation kindred with recessive limb-girdle muscular dystrophy was evaluated by exome sequencing of the proband's DNA. RESULTS: Exome sequencing disclosed 194,618 variants (170,196 SNPs, 8482 MNPs, 7466 insertions, 8307 deletions, and 167 mixed combinations); 71,328 were homozygotic and 123,290 were heterozygotic, with 11,753 non-synonymous, stop-gain, stop-loss, or frameshift mutations occurring in the coding region or nearby intronic region. The cross-referencing of these mutations in candidate genes for muscular dystrophy showed a homozygote mutation c.G674A in exon 4 of LMNA causing a protein change R225Q in an arginine conserved from human to Xenopus tropicalis and in lamin B1. CONCLUSIONS: This technique will be preferred for studying patients with muscular dystrophy in the coming years.

Extended kindred with recessive late-onset Alzheimer disease maps to locus 8p22-p21.2: a genome-wide linkage analysis.

Late-onset Alzheimer disease (LOAD) is a complex genetic disorder. Although genes involved in early-onset forms were discovered more than a decade ago, LOAD research has only been able to point out small effect loci, with the exception of APOE. We mapped the gene predisposing to LOAD in an extended inbred family coming from a genetically isolated region (24 sampled individuals, 12 of whom are affected), completing a genome-wide screen with an Affymetrix10 K single nucleotide polymorphism microarray. Genotyping results were evaluated under model-dependent (dominant and recessive) and model-free analysis. We obtained a maximum nonparametric linkage score of 3.24 (P=0.00006) on chromosome 8p22-p21.2. The same genomic position also yielded the highest multipoint heterogeneity LOD (HLOD) under a recessive model (HLOD=3.04). When we compared the results of the model-dependent analysis, a higher score was obtained in the recessive model (3.04) than in the dominant model (1.0). This is a new locus identified in LOAD, in chromosome 8p22-p21.2 and encompassing several candidate genes, among them CLU and PPP3CC that were excluded by sequencing. The finding of a recessive model of inheritance, consistent with the assumption of inbreeding as a morbidity factor in this population, supports the notion of a role of recessive genes in LOAD.

Clinical-genetic correlations in familial Alzheimer's disease caused by presenilin 1 mutations.

We describe the clinical phenotype of nine kindred with presenile Alzheimer's disease (AD) caused by different presenilin 1 (PS1) point mutations, and compare them with reported families with mutations in the same codons. Mutations were in exon 4 (Phe105Val), exon 5 (Pro117Arg, Glu120Gly), exon 6 (His163Arg), exon 7 (Leu226Phe), exon 8 (Val261Leu, Val272Ala, Leu282Arg), and exon 12 (Ile439Ser). Three of these amino acid changes (Phe105Val, Glu120Gly, and Ile439Ser) had not been previously reported. Distinct clinical features, including age of onset, symptoms and signs associated with the cortical-type dementia and aggressiveness of the disease, characterized the different mutations and were quite homogeneous across family members. Age of onset fell within a consistent range: some mutations caused the disease in the thirties (P117R, L226F, V272A), other in the forties (E120G, H163R, V261L, L282R), and other in the fifties (F105V, I439S). Associated features also segregated with specific mutations: early epileptic activity (E120G), spastic paraparesis (V261L), subcortical dementia and parkinsonism (V272A), early language impairment, frontal signs, and myoclonus (L226F), and late myoclonus and seizures (H163R, L282R). Neurological deterioration was particularly aggressive in PS1 mutations with earlier age of onset such as P117R, L226F, and E120G. With few exceptions, a similar clinical phenotype was found in families reported to have either the same mutation or different amino acid changes in the same codons. This series points to a strong influence of the specific genetic defect in the development of the clinical phenotype.