Non-Hodgkin lymphoma in childhood and adolescence: frequency and distribution of immunomorphological types from a tertiary care center in South India

Manipadam, Marie Therese; Nair, Shalini; Viswabandya, Auro; Mathew, Leni Grace; Srivastava, Alok; Chandy, Mammen

doi:10.1007/s12519-011-0303-7

Cited by 18 publications

(20 citation statements)

References 38 publications

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“…Extranodal sites were observed in 84.1% of cases in this cohort. This trend is in accordance with the results found in the literature [33,34]. However, the prevalence of extranodal NHL in our series was slightly high in comparison with Asiatic series where the prevalence varies from 16 to 40% [34,35].…”

Section: Non-hodgkin Lymphomas and Children supporting

confidence: 93%

Pediatric Non-Hodgkin Lymphomas: First Report from Central Africa

Budiongo

Ngiyulu

Lebwaze

et al. 2015

Pediatric Hematology and Oncology

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Section: Non-hodgkin Lymphomas and Children supporting

confidence: 93%

Pediatric Non-Hodgkin Lymphomas: First Report from Central Africa

Budiongo

Ngiyulu

Lebwaze

et al. 2015

Pediatric Hematology and Oncology

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“…Our approach to identify a large number of new SNPs and to determine their MAF was shown to be a very efficient, cost effective approach in the design of the chip. Although, previous results [6,15] had already shown that the conversion rate of a large proportion of the SNPs identified by Wong et al [5] was very high, the conversion rate of the SNPs identified by our approach surpassed those identified by Wong et al [5]. Of the new SNPs identified in this study, more than 96% could be validated, whereas only 86% of the SNPs present in dbSNP could be validated.…”

Section: Discussioncontrasting

confidence: 63%

“…Nevertheless, numerous studies have used smaller scale SNP assays in chicken, in particular based on Illumina's GoldenGate assay [6-9]. These studies have clearly demonstrated the high validation rate of SNPs identified by Wong et al [5].…”

Section: Introductionmentioning

confidence: 99%

The development and characterization of a 60K SNP chip for chicken

et al. 2011

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BackgroundIn livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important.ResultsWe describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly.ConclusionsThe high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes.

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“…The proportion of T-cell NHL is significantly higher in the Korean pediatric and young adult population (28), Japan (29) and India (19,26), while the frequency of TLL was found to be low in Saudi Arabia (8%), Pakistan (8%) and nearly the same results were obtained from the UK (19%) and Germany (16.1%) (23,24).…”

Section: Discussionmentioning

confidence: 81%