Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders

Abstract

The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.

Benchmarking of bioinformatics tools for the hybrid de novo assembly of human whole-genome sequencing data

“…However, it is worth mentioning that the pursuit of an optimal long-read assembler is shaped by factors such as the sequencing technology and genome complexity. Furthermore, we validated the results across diverse datasets, using not only one of the reference materials from GIAB but also from a routine laboratory sample, underscoring the reproducibility and optimal reliability of adopting a hybrid strategy based on different sequencing technologies (Nurk et al 2022; Díaz-de Usera et al 2022).…”

“…To validate the performance of the best pipeline resulting from the benchmarking, we used human whole-genome data from a routine sample from our laboratory (CAN0003). This sample was included in the reference genetic catalog of the Canary Islands population (CIRdb) that has been described elsewhere (Díaz-de Usera et al 2022). The details for DNA isolation, library preparation, and sequencing were previously described (García-Olivares et al 2021).…”

Digging into the admixture strata of current-day Canary Islanders based on mitogenomes

“…The samples selected for this study self-declared that the four grandparents were born in the same island and that they had no personal history of cardiovascular, metabolic, immunologic, or cancer diseases. 79 The total number of individuals sequenced per island ranged from 52 to 215. By island, from west to east, the number of sequenced individuals was as follows: El Hierro, 106; La Palma, 101; La Gomera, 136; Tenerife, 175; Gran Canaria, 215; Fuerteventura, 52; and Lanzarote, 111.…”

Germline mutations in patients with oral mucosal leukoplakia and squamous cell carcinoma: a prospective observational study

“…Для выделения ДНК использовали диагностический набор QIAamp DNA FFPE Tissue Kit (Qiagen, Германия). Все операции по подготовке ДНК-библиотек к секвенированию выполняются пошагово в строгом соответствии с инструкциями по применению, прилагаемыми производителем (Illumina, Inc., США) к набору реагентов для экзомного секвенирования Illumina Nextera DNA Exome (Illumina, Inc., США) 2,3 [13,14].…”