Discover Glo 2023 - Biologically Relevant Models to Advance your Research

I am an Associate Professor (docent) in Biology with a focus on Limnology. The overarching theme of my research career has been aquatic microbial ecology. I have special interest in understanding the effect of microbial-viral interaction on community assembly and function, the diversity of carbon processing hot-spots within inland water systems and the way microbial carbon processing at such hot-spots happen.
In addition, I have always been dedicated to reveal and address the methodological problems of environmental microbiology to achieve as unbiased view of microbial and viral communities as possible.

Furthermore, I am engaged in science dissemination and outreach. Throughout the years I have organised and participated in diverse outreach activities about microbial diversity and antibiotic resistance. I am also one of the developers of Cure me! an educational game about antibiotic resistance created in collaboration with the Uppsala Antibiotic Center.
Finally, in response to the COVID-19 pandemic, I initiated the measurement of SARS-CoV-2 in the wastewater of Uppsala. I am also the scientific lead of the Environmental Virus Profiling research area of SciLifeLab. The results of our measurements are regularly updated on the CRUSH COVID dashboard and all data is available on the Swedish COVID Data Portal.

Benchmarking of methods for nucleic acid extraction from wastewater

In Sweden the analysis of SARS-CoV-2 virus in wastewater was initiated by independent research groups. The virus content of the sewage measured by these groups showed good correlation with the development of cases and their regular monitoring work was able to predict both the second and third wave of the pandemic in various cities. Through the monitoring work diverse challenges were overcome such as handling the variance in wastewater quality due to the variable weather and large geographic distances of the country, optimization of long-term storage conditions and comparison of fresh and archived samples, and sensitivity improvements to provide optimal surveillance of even small outbreaks in the post-vaccination world. Their collaboration led to the establishment of a capability that today provides surveillance of more than quarter of the population of the country and has embarked on becoming a broad spectrum center of environmental epidemiology.

Jakob has been working at Clinical genetics in Uppsala for about 6 years, where he was quickly put in charge of RT-qPCR and RNA purification. During these years, he oversaw the transfer of the previous RNA purification process of using TRIzol to the more automated Maxwell CSC system.

Arctic Therapeutics and the use of Maxwell in a biotech company, genetic sequencing and ongoing clinical trials.

Arctic Therapeutics is an Iceland-based drug discovery and development company that is focused on identifying the genetic underpinnings of both rare and common disease to develop novel and innovative therapies. Its drug pipeline consists of five drug development projects with a wide range of applications. AT's first POC study was based on a founder mutation out of Iceland due to cystatin C mutation (L68Q), which results in accelerated amyloid deposition often clogging brain vessels and causing stroke and/or early dementia, a serious condition called Hereditary Cystatin C Amyloid Angiopathy (HCCAA), this therapy may inform future Alzheimer’s treatment; and treatment of genetically-related similar CAA diseases in multiple other countries. In this talk, we will share our experiences with the Maxwell device in AT's clinical trials in genomic and drug discovery.

Louise Ambye is a biochemist, Ph.D. at the Department of Clinical Biochemistry and Hvidovre Hospitals NIPT Center, Amager Hvidovre Hospital, Denmark with many years of experience in research in prenatal genetic testing in ongoing pregnancies and pregnancy losses. By focusing on the Non-Invasive prenatal tests (NIPT), Louise and her team have developed an automated in-house pipeline for screening for chromosome abnormalities in fetuses from blood samples from their mothers.   

Validation of a Cell-free fetal DNA (cffDNA) test for detection of chromosome abnormalities in fetuses from pregnancy losses: A part of the Copenhagen Pregnancy Loss (COPL) study

L. Ambye^1,2, L. Werge^1,2, T.S. Hartwig³, S. Bliddal³, E.R. Hoffmann⁴, F.S. Jørgensen^2,3, H.S. Nielsen²

1.Department of Clinical Biochemistry, Amager Hvidovre Hospital, Denmark

2.Hvidovre Hospitals NIPT Center, Denmark

3.Department of Obstetrics and Gynecology, Amager Hvidovre Hospital, Denmark

4.Department of Cellular and Molecular Medicine, University of Copenhagen, Denmark

Background: Non-invasive prenatal test (NIPT) has since 2017 been offered to ongoing pregnant women in Denmark with a high-risk of chromosome abnormalities. The test is used for screening of the most common chromosome abnormalities and is based on a blood sample from the mother containing cell-free fetal DNA (cffDNA) from apoptotic cytotrophoblasts in the placenta. In Denmark one in four pregnancies end in a pregnancy loss. The loss affects couples mentally and the women are in an elevated risk for later health consequences and recurrent pregnancy loss, especially women with euploid pregnancies losses compared with aneuploid losses. The current knowledge of pregnancy losses is poor and most genetic studies have been performed on pregnancy tissues, which might be contaminated with maternal tissue and can be difficult to collect.

Aim: The Copenhagen Pregnancy Loss study is a large initiative with the aim to explore the causes of pregnancy losses. One aim of this project is to develop an easy and quick pipeline for fetal chromosome evaluation in pregnancy losses based on cffDNA in maternal blood and evaluate the method against analyses on pregnancy tissue.

Method: Blood samples were drawn in Streck tubes from 1000 women with pregnancy loss and pregnancy tissue were collected from 333 of these women for validation of the cffDNA-test. Blood samples were centrifuged twice, and plasma were stored at -20°C until extraction of cell-free DNA (cfDNA). CfDNA were purified from 2 ml plasma using MaxWell RSC cfDNA plasma kit and a MaxWell RSC Instrument from Promega. Libraries were built using TruSeqNano DNA LT Library Prep Kit and the libraries were sequenced by Massive Parallel Sequencing on a HiSeq1500 with TruSeq Rapid SBS kit 50 cycles (RS) from Illumina. Data analysis for genetic status were performed using the programs WISECONDOR/DEFRAG/SeqFF. DNA from tissue were extracted and sequenced by shallow sequencing on a NextSeq550.   

Results: Comparing the genetic results from the cffDNA-test with the results from pregnancy tissue it showed a sensitivity for aneuploidy detection of 81% (95% CI 73-87) and a specificity of 91% (95% CI 84-95) with an accuracy of 85% for the cffDNA-test. Among the 1000 cffDNA tests 45% were euploid, 45% were aneuploid and 10% were inconclusive (no-calls). The most common chromosome abnormalities were trisomy 16 (n=91), trisomy 22 (n=41) and monosomy X (n=86). 105 (32%) of the 333 women either did not manage to collect pregnancy tissue or collected a sample classified with unknown tissue because of poor quality, giving a high risk of maternal contamination.   

Conclusion: The study shows that the cffDNA-test can be used as a pregnancy tissue independent alternative and that 50% of pregnancy losses can be explained by chromosome abnormalities. It is an easy, quick, and cheap test to distinguish women with either euploidy or aneuploidy pregnancy losses. In case of an euploidy result, this may help the woman continuing with further tests to explain her loss and hopefully cure or prevent recurrent loss.

^Reference:

^{Hartwig TS, Ambye L, Gruhn JR, Petersen JF, Wrønding T, Amato L et. al. COPL consortium. Cell-free fetal DNA for genetic evaluation in Copenhagen Pregnancy Loss Study (COPL): a prospective cohort study. Lancet. 2023;4:762-771.}

I have always been interested in working on somatic cancer genetics. I teach a lot of doctors, nurses, and students to understand the importance of genetics in confirming the diagnosis of cancer, and assessing prognosis and treatment. I am also involved in many research groups. Cooperation with doctors, other laboratories pharmaceutical companies, and product manufacturers is also part of my job description.

The use of Maxwell in the isolation of challenging cancer samples

In our laboratory, we use Maxwell to isolate DNA from blood, bone marrow, mononuclear cells, cerebrospinal fluid, pleural fluid, ascites fluid and paraffin samples. Some of the samples are pre-treated before isolation. We also use Maxwell to isolate RNA mainly from tissue, blood and bone marrow. The concentration and purity of DNA and RNA is determined with a NanoDrop spectrophotometer or Qubit. In my presentation, I will share our laboratory's experiences with the Maxwell device, its benefits and challenges.