P6012 Use of targeted next generation re-sequencing in the identification of polymorphisms in the bovine collagenous lectin gene family
Notice bibliographique
Résumé
Collagenous lectins bind carbohydrate motifs on pathogens, leading either to the activation of the lectin complement pathway or to the opsonization or agglutination of pathogens. They play an important role in innate immunity against a variety of bacteria, viruses, and fungi. Functionally altered proteins resulting from genetic mutations in collagenous lectins have been shown in other species to predispose animals to infectious disease. This study aimed to 1) identify genetic variation in the bovine collagenous lectin genes; and 2) determine whether polymorphisms were associated with an increased susceptibility to infectious disease. We used pooled, targeted next generation re-sequencing to identify variants in the bovine collagenous lectin genes. Cattle submitted for post-mortem examination at the University of Guelph were classified as normal (n = 40) or diseased (n = 80) based on the presence or absence of infectious disease. Cattle were placed into groups of 5 based on the similarity of diagnosis, and an equal amount of DNA from each animal was pooled. The collagenous lectin genes (including three unique to bovids) along with 3 kb of downstream DNA and up to 50 kb of upstream DNA were targeted for re-sequencing. The sequencing library was prepared with a Roche Nimblegen EZ Developer kit and sequenced on an Illumina MiSeq. In total, 4.6 Gb of usable sequence data was obtained with an average read depth of 42x/cow over the target region. Following application of quality control filters, 6525 single nucleotide variants (SNVs) were found, including 510 not reported in dbSNP. This included 3948 upstream region SNVs, 2672 downstream region SNVs, and 411 intronic SNVs. Within exons, 107 SNVs, including 54 missense mutations, were identified. In silico analysis of the missense mutations identified 16 SNVs with significant potentially disruptive effects on protein structure. A mutation in MBL2, resulting in a P42Q change in the collagen-like domain, holds particular interest, as similar mutations in orthologous genes have been shown to have impact on susceptibility to disease. Allele frequencies between the normal and diseased populations were compared and the potential impact of promoter SNVs investigated. This study demonstrates that pooled, targeted re-sequencing is a cost effective method of polymorphism identification and discovery in cattle. We identified 510 previously unreported SNVs, as well as 16 mutations potentially affecting collagenous lectin structure or function. These SNVs will help in our understanding of the genetics of disease susceptibility, and represent potential candidates for genetic selection.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,002 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,001 |
| 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) | 0,000 | 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 tête enseignante, 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 ».