Impact of whole genome amplification on analysis of copy number variants

Large-scale copy number variants (CNVs) have recently been recognized to play a role in human genome variation and disease. Approaches for analysis of CNVs in small samples such as microdissected tissues can be confounded by limited amounts of material. To facilitate analyses of such samples, whole genome amplification (WGA) techniques were developed. In this study, we explored the impact of Phi29 multiple-strand displacement amplification on detection of CNVs using oligonucleotide arrays. We extracted DNA from fresh frozen lymph node samples and used this for amplification and analysis on the Affymetrix Mapping 500k SNP array platform. We demonstrated that the WGA procedure introduces hundreds of potentially confounding CNV artifacts that can obscure detection of bona fide variants. Our analysis indicates that many artifacts are reproducible, and may correlate with proximity to chromosome ends and GC content. Pair-wise comparison of amplified products considerably reduced the number of apparent artifacts and partially restored the ability to detect real CNVs. Our results suggest WGA material may be appropriate for copy number analysis when amplified samples are compared to similarly amplified samples and that only the CNVs with the greatest significance values detected by such comparisons are likely to be representative of the unamplified samples.

Cytogenetic abnormalities in MALT lymphomas and their precursor lesions from different organs. A fluorescence in situ hybridization (FISH) study

AIMS

To analyse the possible activation of distinct molecular pathways in mucosa-associated lymphoid tissue (MALT) lymphoma, we determined the prevalence of trisomies 3, 12, 18 in MALT lymphomas from different organs, as well as the prevalence of translocations of the MALT1 gene in a subset of primary breast MALT lymphomas. We compared the numerical cytogenetic alterations in lymphomas, precursor lesions and in normal non-haematolymphoid tissue from the same organs.

METHODS AND RESULTS

Forty-two samples of paraffin-embedded tissue (29 MALT lymphomas from stomach, breast, parotid and thyroid; two Sjögren's syndrome; two Hashimoto's thyroiditis and nine reactive samples) were studied by fluorescence in situ hybridization (FISH). Analysed together, the cases of gastric, parotid and thyroid MALT lymphomas presented trisomy 3 in 46%, trisomy 12 in 28% and trisomy 18 in 21% of the cases. In contrast to other locations, trisomy 3 was not present in the majority of the cases of primary breast MALT lymphomas. None of the nine breast cases presented MALT1 gene rearrangements. Half of the cases of preneoplastic lesions exhibited trisomy 3 and trisomy 12; none exhibited trisomy 18.

CONCLUSIONS

Trisomy 3 is the most frequent numerical abnormality in gastric, parotid and thyroid but not in primary breast MALT lymphomas. MALT1 gene rearrangements are also rare in this location, suggesting that distinct molecular pathways may be activated in breast cases.

Long-term follow-up of bulky classic Hodgkin lymphoma managed with ABVD and PET-guided RT demonstrates excellent outcomes in PET-negative cases

The outcome of 221 patients with bulky (≥10 cm) classic Hodgkin lymphoma (cHL) treated with doxorubicin, bleomycin, vinblastine, dacarbazine and consolidative radiotherapy (RT) only in those with a positive end-of-treatment (EOT) positron emission tomography (PET) scan was evaluated. With a median follow-up of 9.6 years, 5- and 10-year progression-free survival (PFS) in EOT PET-negative cases were 94.0% and 90.4%, respectively, and in PET-positive cases, 5/10-year PFS was 64.6% (p < 0.001), with 15% overall receiving RT. Five-year PFS for Deauville (D) score DX/D1-3 was 93.6%, compared with D4 66.7% (p < 0.001) and D5 33.3% (p < 0.001). Omission of RT in EOT PET-negative cases is associated with excellent long-term outcomes in bulky cHL.