Human leukocyte antigen typing using buccal swabs as accurate and non‐invasive substitute for venipuncture in children at risk for celiac disease

Adriaanse, Marlou P. M.; Vreugdenhil, Anita; Vastmans, Véronique; Groeneveld, Lisette; Molenbroeck, Stefan J. J.; Schött, D; Voorter, Christina E.M.; Tilanus, Marcel G.J.

doi:10.1111/jgh.13331

Cited by 5 publications

(5 citation statements)

References 18 publications

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“…These limitations are challenging for high volume donor recruitment typing, particularly when participants are dispersed geographically. Buccal swabs, on the other hand, are considered a convenient alternative for collecting genetic material, as they are relatively inexpensive, noninvasive and can be mailed out for self-collection and return-mailed for centralized testing [24,25]. In our study, DNA yield from buccal swabs was approximately six times lower than DNA isolated from blood samples.…”

Section: Discussionmentioning

confidence: 75%

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples

Yin¹,

Lan

Nguyen³

et al. 2016

PLoS ONE

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BackgroundUnambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA.MethodsMultiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3’ UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing.ResultsUsing this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%).ConclusionLong-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation.

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Section: Discussionmentioning

confidence: 75%

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples

Yin¹,

Lan

Nguyen³

et al. 2016

PLoS ONE

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“…In recent years, genetic testing has moved away from reliance upon invasive blood sampling toward user-friendly buccal swabs (42, 43). From commercially available at-home genetic testing kits (e.g., , ) to paternity testing in the NICU, the ease with which sufficient quality and quantity of DNA samples can be obtained has markedly improved (43).…”

Section: Salivary “Omics”mentioning

confidence: 99%

Salivary Diagnostics in Pediatrics: Applicability, Translatability, and Limitations

Hassaneen

Maron

2017

Front. Public Health

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In the last decade, technological advances, combined with an improved appreciation of the ability of saliva to inform caregivers about both oral health and systemic disease, have led to the emergence of salivary diagnostic platforms. However, the majority of these assays have targeted diseases that more commonly affect the adult population, largely neglecting infants and children who arguably could benefit the most from non-invasive assessment tools for health monitoring. Gaining access into development, infection, and disease through comprehensive “omic” analyses of saliva could significantly improve care and enhance health access. In this review, we will highlight novel applications of salivary diagnostics in pediatrics across the “omic” spectrum, including at the genomic, transcriptomic, proteomic, microbiomic, and metabolomic level. The challenges to implementing salivary platforms into care, including the effects of age, diet, and developmental stage on salivary components, will be reviewed. Ultimately, large-scale, multicenter trials must be performed to establish normative biomarker values across the age spectrum to accurately discriminate between health and disease. Only then can salivary diagnostics truly translate into pediatric care.

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“…LBT is highly specific and it has been considered the golden standard for the diagnosis of lactose intolerance; it however requires the patients to spend at least 4 h in the hospital; moreover, patients have to prepare themselves along the previous days. Genetic testing is a standard technique for the diagnosis of primary adult lactase persistence; it is a quick test, based on DNA extraction, usually from an EDTA blood sample or buccal swab [13], followed by real-time PCR protocol for the detection of a single SNP per reaction and Sanger sequencing, that is the most used method [14][15][16][17]. Other approaches have recently been developed, based on different techniques, like pyrosequencing [18], melting curve analysis [19], or loop-mediated isothermal amplification and melting curve analysis [20].…”

Section: Introductionmentioning

confidence: 99%

Development of a novel SNP assay to detect lactase persistence associated genetic variants

et al. 2021

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Background In adulthood the activity of the lactase enzyme is inherited as autosomal dominant form associated to Single nucleotide polymorphisms (SNPs). The present research was aimed to develop a novel genetic method to test lactase non persistence more powerfully. Methods and results In our study, we selected eight different SNPs that are associated with lactase persistence from Caucasian, Arabian Bedouins, sub-Saharian Africans and Asian populations to set up an approach to detect all the eight different SNPs at the same time in the same sample. This technique is centred on the identification of SNPs with a single nucleotide primer extension method using Sanger sequencing and capillary electrophoresis. Conclusions Our method allowed us to check the genotype asset of eight SNPs related to lactase persistence simultaneously and in a very efficient manner. It could be applied to a higher number of SNPs in a single reaction.

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Human leukocyte antigen typing using buccal swabs as accurate and non‐invasive substitute for venipuncture in children at risk for celiac disease

Cited by 5 publications

References 18 publications

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples

Salivary Diagnostics in Pediatrics: Applicability, Translatability, and Limitations

Development of a novel SNP assay to detect lactase persistence associated genetic variants

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