Structural Variation within the Beta-Globin Gene Cluster Among HbS Haplotype Groups
Notice bibliographique
Résumé
Abstract BACKGROUND The severity of sickle cell anemia (SCA) has been associated with five specific haplotypes in the beta globin cluster, identifiable by distinct patterns of restriction fragment length polymorphism (RFLP). These RFLP-defined haplotypes, named according to the region where they were first discovered - Central Africa region (CAR), Benin, Senegal, Arabic-Indian, and Cameroon - suggested that the sickle cell mutation arose recently at least four independent times in Africa, each time on a different genetic background, and again in India - the Multi-centric Sickle Cell Model. The beta-globin locus, however, is prone to extensive structural rearrangements, and alongside observations of ancestral sequence haplotypes extending several hundreds of kilobases beyond the beta globin cluster, it has been suggested that there is more cis-variation in the beta-globin gene cluster than is evident from RFLP analyses, and current definitions of RFLP haplotypes may not accurately reflect the ancestral origin of the sickle mutation. This undescribed cis-variation is important to understanding inter-individual phenotype variation associated with the different haplotypes. To better define this variation, we have undertaken extended, long-range molecular haplotyping of the beta-globin cluster on differing RFLP haplotype backgrounds using real time single molecule sequencing (SMS). The SMS approach generates long, unbroken reads with uniform coverage, thereby allowing for detailed molecular phasing of RFLP haplotypes and identification of local structural variation that would otherwise be hidden within the complex repetitive elements of the beta-globin cluster. In so doing, we plan to evaluate the molecular evidence for a single origin for the sickle cell allele and identify potential cis-acting, disease-modifying, candidate variants within the beta globin cluster. METHODS DNA from 200 SCA patients from three countries in sub-Saharan Africa - Nigeria, Cameroon, and Kenya - were collected after informed consent. RFLP analysis revealed the majority of the patients to be homozygous for the Benin and CAR haplotypes, with a smaller sampling of Cameroon, Senegal, and Atypical haplotypes. From this group we selected 40 samples - representing the four main classical RFLP haplotypes in sub-Saharan Africa - were selected for SMS. PCR was used to tile barcoded amplicons across the cluster. SMS was performed on a Sequel machine (Pacific Biosciences). The resulting FASTQ sequences were de-multiplexed, read quality control filters were applied, and mapped to human reference genome Hg38, prior to annotation and calling of single nucleotide variants (SNV) and structural variants (SV). RESULTS Analyses have so far identified 227 insertions, 18 deletions, 7 duplications, 76 inversions and 13 translocations from long-read analyses of the initial 40 samples; the vast majority of these variants are not described in public variant databases. Atypical haplotypes demonstrated more translocation and duplication events than other haplotypes. Insertions ~48 kb upstream of the beta-globin locus control region and 1.3 kb upstream of gamma globin gene 2 (HBG2) were observed on 50% of Senegal and 45% of CAR haplotypes. Also, recurrent insertions ranging between 32bp and 1,184bp in length, 2.3 kb downstream of the beta globin gene (HBB), were seen on 50% of the Benin and 54% of the CAR haplotypes, but only once on Senegal haplotypes. CONCLUSIONS Our findings suggest there are more cis-SVs within the beta-globin gene cluster than previously described. Work to validate these SVs using orthogonal methods and complete similar analyses of SNVs is ongoing. Variation outside of the gene cluster will also be integrated with RFLP and within-cluster molecular haplotypes to investigate the ancestral origin of the mutation, and validated cis-acting variants will be used to identify markers associated with proxies of SCA disease modification. Disclosures No relevant conflicts of interest to declare.
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Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,002 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».