Vavoulis, D. V. | Search bioRxiv

bioRxiv2019

Differential genomic and transcriptomic events associated with high-grade transformation of Chronic Lymphocytic Leukemia

The transformation of chronic lymphocytic leukemia (CLL) to high-grade diffuse large B-cell lymphoma (DLBCL), also called Richters Syndrome (RS), is a rare cancer with dismal prognosis. Drug discovery for RS is hampered by the lack of suitable experimental models, and effective therapies remain elusive rendering RS an area of high unmet clinical need. We performed whole genome sequencing (WGS) to interrogate paired CLL and RS samples from 17 patients enrolled in a prospective multicenter Phase 2 clinical trial (CHOP-OR) and we found that subclones affected by mutations in MAPK and PI3K pathways show a high expansion probability during transformation. We also demonstrate for the first time that non-coding mutation clusters in a PAX5 enhancer, situated 330kb upstream from the transcription initiation site, correlate with transformation. Finally, we confirm our findings by employing targeted DNA sequencing (TGS) and RNA expression profiling on an extended cohort of 38 patients.\n\nStatement of significanceThrough integrated analysis of WGS, TGS and RNA expression data, we identified drivers of transformation not previously implicated in RS, which can be targeted therapeutically and tested in the clinic. Our results have informed the design of a new clinical platform study, which is now open to recruitment in the UK.

genomics↗

bioRxiv2019

A method for non-invasive prenatal diagnosis of monogenic autosomal recessive disorders

Non-invasive prenatal testing (NIPT) to date is used in the clinic primarily to detect foetal aneuploidy. Few studies so far have focused on the detection of monogenic autosomal recessive disorders where mother and foetus carry the same mutation. In particular, NIPT is currently not available for the detection of Sickle Cell Anaemia (SCA), the most common monogenic disorder world-wide and the most common indication for invasive prenatal testing in high-income countries. Here, we report the clinical validation of a novel diagnostic approach that combines ultra-sensitive amplicon-based sequencing of cell-free DNA (cfDNA) with internal controls and bias factor correction to calculate the probability for the presence of allelic imbalance from maternal plasma without prior knowledge of the paternal genotype. Identification of the foetal genotype was determined using a hierarchical probabilistic model based on the relative number of reads from the sequencing, along with the foetal fraction. NIPT was performed on a cohort of 57 patients, all of whom had previously undergone invasive prenatal testing so that the foetal genotype was known. Overall, NIPT demonstrated 100% sensitivity and negative predictive value for foetal fractions higher than 0.5%, and 100% specificity and positive predictive value for foetal fractions higher than or equal to 4%. Our methodology can be used as a safe, non-invasive screening tool in any clinical scenarios where early prenatal diagnosis of SCA or other recessive disorders is important.

genomics↗