Laboratory for Cytogenetics and Genome Research – KU Leuven

Human genome study for a healthier population

The Laboratory for Cytogenetics and Genome Research at the KU Leuven leads a translational Genomic Medicine program on the interface between clinical practice and strategic fundamental research, in a tight junction with the Center for Human Genetics (CME: Centrum Menselijke Erfelijkheid). They are embedded in the Leuven University Hospital and associated with the university genetic diagnostic unit.

The CME is well-recognized as a leading genetics and genomics hub, with over 10,000 contacts every year with patients suffering various genetic diseases. This represents more than 25% of the genetic activities in Belgium. The diagnostic activities of the center comprise both constitutional and cancer genetic diagnostics. Over 60,000 samples are processed yearly, which makes the center one of the largest academic genetic diagnostic laboratories in Europe.

Novel approaches for postnatal diagnosis

The program has three discrete lines of research and valorisation. The first line focuses on novel approaches for genome diagnostics, using whole genome sequencing.

“We lead the transition from genetic testing to genomic medicine, from a single gene disorder to genome-wide analysis. This translation goes together with the continuous development and integration of state-of-the-art technologies in the research and diagnostic programs,” says lab leader Prof. Joris Vermeesch.

“Thanks to decreasing sequencing costs, ever-increasing amounts of genomic data become available, enabling the detection of ever more genetic disorders. We continuously invest in state-of-the-art sequencing equipment. Recently, we obtained long-read sequencing technologies that enable the identification of structural variants and complex/repetitive regions of the genome, and the detection of the methylation state of those regions. This allows a multi-omics analytical approach at very reduced cost and with higher efficiency.”

“Challenges include the development and implementation of a toolbox enabling the telomere-to-telomere analysis, ever decreasing amounts of input (to single cell) and databasing variation. Targeting relevant control and disease populations also is a challenge in the coming years. The mere existence of personalised medicine is dependent on clinical/omics data production and foremost efficient sharing among stakeholders.”

Vermeesch’ team leads large scale national programs to elucidate rare diseases, including the BeSolveRD (BelgianSolveRareDisease) project and the Belgian genome Biobank and participates in large scale international projects such as the international Brain Behaviour consortium, the EASI-Genomics (a Horizon 2020 infrastructure project (RIA)) and the B1M+ working and 1M+ program. “Furthermore, we participate in genomic medicine data sharing programs.”

Single cells and early embryos

The second research line is on genomics of single cells and early embryos to enable embryo selection. “Currently, genetic and genomic analyses are generally performed on DNA extracted from large numbers of cells,” Vermeesch explains. “Most analyses provide an average genetic profile derived from multiple cells. In many instances, the analysis of single cells is required and/or would help our biological understanding. For example, analysis of embryos for preimplantation genetic diagnosis requires the analysis of a single or a few cells.”

Several methods for single-cell genome analysis based on microarray and next-generation sequencing platforms developed by the team led to seminal novel clinical applications in routine genetic diagnostics.

“We develop technology for low-cost genome-wide genotyping of single cells. Novel sequencing technologies now enable assessing the variation of several 100,000’s targets at a genome-wide level. We delivered proof-of-principle for single cell genotyping-by-sequencing, representing a straightforward, quick and reproducible workflow for cost-effective NGS-based genotyping of individual cells. This novel technology also allows access to genomic regions that are inaccessible to sequence capture approaches. In addition, we developed proprietary methods to interpret and improve the accuracy of those genotypes.”

Liquid biopsies

The third research line focuses on liquid biopsies, allowing the non-invasive detection of genetic alterations caused by pregnancy, cancer or other diseases. Dying cancer cells often shed their DNA in the bloodstream. As a consequence, circulating cell-free DNA becomes a valuable biomarker for cancer diagnosis and monitoring of treatment response. It has also been paramount for monitoring fetal health and specifically aneuploidy (non-invasive prenatal diagnosis).

We were the first European independent laboratory to offer pregnant women a non-invasive prenatal test (NIPT). Currently, over 25,000 samples are processed each year. Cancer patients are currently monitored after treatment using imaging methods, which are expensive and laborious to use in large patient cohorts.

In many cancers, where surgical removal of metastases increases survival, such as colorectal cancer (CRC), earlier detection of metastatic processes would benefit the patients. Circulating tumor DNA (ctDNA) is another approach to monitor cancers. We developed algorithms and approaches to analyze with high precision liquid biopsy samples at the genomic level, while we have access to a multitude of samples (prenatal, cancer, immuno,…).

Based on our initial results of cancers in pregnant women, we are involved in several national and European programs rolling out a comprehensive automated liquid biopsy genomic platform leveraging stratified medicine. We are in the process of uncovering multiple new relevant clinical diagnostic opportunities and broadening the scope of our ctDNA tool towards applications in prenatal medicine, non-invasive pan-cancer early detection, organ transplant monitoring by liquid biopsy, immune activity response monitoring in autoimmune diseases, immune response monitoring during cancer immunotherapy, mutation detection by liquid biopsy in cancer and rare disease detection.”

Genomics core

The single cell and genomics core facility, a collaborative effort of the Center for Human Genetics at KU Leuven and Leuven University Hospital, is a knowledge and technology platform to make available state-of-the-art technologies, protocols and bioinformatic pipelines for research and diagnostics. It facilitates access to different sequencing technologies and shares expertise in genomic sequence analyses and data processing.

The genomics core instrumentarium for high-capacity sequencing consists of 3 newly acquired NovaSeq6000, 2 HiSeq4000, 1 Illumina HiSeq2500, 2 MiSeqs, a NextSeq500 and the long-read sequencers Oxford nanopores Promethion and a PacBio sequencer (SequeII); for sample automation, QC and sample preparation: a Caliper Sciclone, 2 Hamilton Star robots, a Labcyte acoustic liquid handler, a BluePippin fragment separator, a fragment analyser, a Covaris sonicator; for single forms (10X genomics (10X Chromium), C1 Fluidigm, DEP-Array for rare cell isolation), custom-built liquid handling robotics (Hamilton, Mosquito); and instruments for array technology: a Sequenom MassArray for medium-throughput SNP typing, an Illumina iSCAN for high-throughput SNP and CpG genotyping and Agilent CGH scanning platforms.

“Additionally, we use Google Genomics for computer storage and data handling. This allows greater parallelization and elastic scaling. We service over 150 different clients yearly.”