THE LOGSDON LAB
WELCOME TO
THE LOGSDON LAB
We use long-read sequencing and synthetic biology approaches
to investigate the variation, evolution, & function of
human centromeres and their role in health & disease
What are centromeres,
and why are they so fascinating?
Centromeres are specialized regions on each chromosome that mediate the segregation of sister chromatids during cell division. Errors in chromosome segregation can cause aneuploidy, or an imbalance in chromosome number, which can result in cancer, infertility, and birth defects. Although centromeres are essential chromosomal regions, their sequence has remained unresolved in the human genome for the past two decades. The lack of complete centromeric sequences has limited our understanding of the role these regions play in essential cell biological processes required to maintain genome integrity and sustain life. During her postdoctoral training, Dr. Logsdon developed wet- and dry-lab methods to determine the first complete sequence of a human autosomal centromere (Logsdon et al., Nature, 2021). This work led to the complete sequence of all human centromeres (Altemose et al., Science, 2022) and, ultimately, the completion of the human genome (Nurk et al., Science, 2022).
The complete sequence of each human centromere provides an unprecedented opportunity to determine their variation and evolution for the first time. As such, the Logsdon Lab aims to uncover the genetic and epigenetic variation of centromeres among the human population and in diseased individuals, develop a model of human centromere variation, and use this model to study their basic biology and function. In addition, the Logsdon Lab plans to reconstruct the evolutionary history of centromeres over the last 25 million years using phylogenetic and comparative approaches with both human and non-human primate species. Finally, the Logsdon lab will apply our discoveries of centromeres to design and engineer new ones on human artificial chromosomes (HACs). This effort will build on Dr. Logsdon's previous success in engineering HACs (Logsdon et al., Cell, 2019) and has the potential to revolutionize scientific research and medicine through the design of custom chromosomes and genomes. Together, our lab's research will advance our understanding of the complex biology of human centromeres and will generate HACs that have the potential to fundamentally transform scientific research and medicine.
Research interests
Centromere variation among the human population
With advances in long-read sequencing technologies and genome assembly algorithms, we are now in an era where the systematic assembly of centromeres is becoming a reality. The complete assembly of centromeres enables the study of their sequence and structural variation for the first time, and it allows for the precise mapping of histones and other centromeric proteins that were previously unmappable. As such, we are standing on the precipice of uncovering the complex biology of centromeres through the discovery of their genetic and epigenetic landscapes. The Logsdon Lab will lead the effort in this area by sequencing and assembling hundreds of human genomes from both healthy and diseased individuals, determining their centromeric genetic and epigenetic variation, and experimentally testing how this variation impacts centromere function. This work is foundational and will greatly advance our understanding of centromere biology and its role in chromosome segregation during cell division. This work will be done in close collaboration with the Human Pangenome Reference Consortium (HPRC) and the Human Genome Structural Variation Consortium (HGSVC).
The first view of human centromere variation among two complete sets of centromeres. These centromeres show a remarkable level of variation in the size and structure of their a-satellite HOR arrays, as indicated by the colorful regions shown between each pair of chromosomes. Additionally, 16 out of 23 centromeres show variation in the location of the kinetochore, marked by the presence of nucleosomes containing the histone H3 variant, CENP-A (dark red dot), with six having kinetochores separated by over 500 kbp of sequence. Adapted from Logsdon et al., Nature, 2024.
Centromere evolution among primate species
The complete sequence, structure, and epigenetic landscape of six sets of centromeres from four primate species (human, chimpanzee, orangutan, and macaque). Comparative analysis of these six sets of centromeres reveal diverse a-satellite HOR organization and structures and distinct species-specific differences. Adapted from Logsdon et al., Nature, 2024.
Centromeres are among the most rapidly evolving regions of the genome, with a mutation rate at least four-fold greater than the unique portions (Logsdon et al., Nature, 2021). This rapid evolution leads to variation in a‑satellite sequence and structure, and it contributes to the emergence of new a-satellite repeats. The forces that shape the evolution of human centromeres are not well understood, and this is largely due to a lack of complete sequence assemblies of centromeres from other primates. The Logsdon Lab will fill this gap in knowledge by sequencing and assembling centromeres from diverse primate species and using these assemblies to reconstruct the evolutionary history of centromeres over the last 25 million years. We will initially focus on the bonobo, chimpanzee, gorilla, orangutan, and macaque species but plan to expand to other primates that comprise the lesser apes and New World monkeys. This work will be done in close collaboration with the Telomere-to-Telomere (T2T) Consortium, who is planning to generate the first complete reference genomes for nearly all primates. We will also work with our long-standing collaborators who have expertise in primate centromere evolution and pangenomics.
Engineered centromeres on human artificial chromosomes
Human artificial chromosomes (HACs) have the potential to revolutionize scientific research and medicine through the development of numerous radical advancements, such as engineered viral immunity and cancer resistance in cell lines as well as cost-effective vaccine and pharmaceutical development. The Human Genome Project-Write is leading the way in this area by proposing to synthesize human chromosomes and genomes from scratch, building on previous successes in budding yeast. Among the many potential hurdles in translating success from yeast to human, perhaps the greatest is the centromere. Unlike yeast, human centromeres are comprised of hundreds of thousands of a-satellite repeats, which have been challenging to sequence and assemble for the past
Metaphase chromosome spreads containing a human artificial chromosome (HAC; green). HACs are engineered mini-chromosomes that acquire a functional centromere and are stably maintained in human cells. A functional centromere is indicated by the presence of the centromeric histone H3 variant CENP-A (red). Scale bar = 10 microns. Adapted from Logsdon et al., Cell, 2019.
two decades. The lack of complete assemblies of these regions has hindered our ability to identify sequences that can form a centromere on a HAC, such as those associated with centromeric chromatin and the kinetochore. Because the Logsdon Lab will resolve the sequence of hundreds of human centromeres, we are in an ideal position to identify sequences that may be able to form a centromere on a HAC. Therefore, we plan to identify centromere-competent DNA sequences from natural human centromeres and test them for centromere formation and long-term stability on a HAC. This work will lay the groundwork for the construction of future synthetic human chromosomes and genomes that may fundamentally transform scientific research and medicine.
Featured publications
In the news
Photo credit: Michael Abbey/Science Source
Photo credit: Oxford Nanopore Technologies
Photo credit: Kendra Hoekzema
Image credit: George Retseck/The Scientist
Team
Email: glogsdon@pennmedicine.upenn.edu
Pronouns: she/her
Social media:
Glennis Logsdon, Ph.D.
Principal Investigator
Dr. Logsdon is an Assistant Professor in the Department of Genetics and a Core Member of the Epigenetics Institute at the University of Pennsylvania Perelman School of Medicine. She performed her postdoctoral training at the University of Washington School of Medicine with Dr. Evan Eichler, where she studied the sequence, structure, and evolution of human centromeres using long-read sequencing and computational approaches. Before that, she obtained her Ph.D. in Biochemistry and Molecular Biophysics in 2018 from the University of Pennsylvania Perelman School of Medicine, where she studied centromere establishment on human artificial chromosomes with Dr. Ben Black. She is involved in several national consortia, including the Telomere-to-Telomere (T2T) consortium, Human Pangenome Reference Consortium (HPRC), and Human Genome Structural Variation Consortium (HGSVC). She also works with non-profit, patient-led organizations, such as Project 8p, to better understand complex structural variation in the human genome.
Shu-Cheng Chuang, Ph.D.
Research Specialist
Dr. Shu-Cheng Chuang is a research specialist in the Logsdon Lab. She completed her Ph.D. at the University of Hawaiʻi at Mānoa in 2023, focusing on comparative genomic and gene function analyses of phytobacteria. In addition to her work on prokaryotic genomes, she has previous experience with fungal genomes and has conducted research on transcriptome characterization and gene expression profiles of the pathosystem while at the Agricultural Biotechnology Research Center of Academia Sinica, Taiwan. Her research interests include short- and long-read sequencing, phylogenetic and phylogenomic analyses, and microbial taxonomy. In her free time, she enjoys traveling, outdoor activities, and watching dramas.
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Keisuke (Keith) Oshima
Bioinformatician
Keith is a bioinformatician in the Logsdon Lab. He completed his B.S. in Microbiology at the University of California Santa Barbara in 2020 and taught himself programming by automating tasks in the lab. Building on this as a research intern at the National Marrow Donor Program, in 2022, he automated and optimized an HLA haplotype prediction pipeline on AWS for their registry of 5 million donors. He is passionate about building reproducible, easy-to-use software and is interested in learning and gaining experience in long-read sequencing and genome assembly. In his free time, he enjoys cooking, playing indie games, and using programming to learn new things.
Savana Hadjipanteli
Graduate student
Savana is a Genetics & Epigenetics Ph.D. student in the Cell and Molecular Biology program. She joined the Logsdon Lab in Fall 2024. She received a B.S. in Biology from Case Western Reserve University in 2021, where she studied the effects of structural variants in D. melanogaster meiotic recombination. She then spent time as a lab technician at the University of Houston studying transposable elements and piRNA evolution in flies. Her interests now pertain to the diversity and function of non-coding RNAs derived from repetitive sequences, specifically those from human centromeres. Outside of the lab, Savana enjoys traveling (anywhere), reading (speculative fiction and indie comics), and knitting/crocheting.
Mohamed Imran, Ph.D.
Postdoctoral fellow
Dr. Mohamed Imran is a postdoctoral fellow in the Logsdon Lab. He completed his Ph.D. at CSIR-IGIB, New Delhi, in 2024 under the supervision of Dr. Sridhar Sivasubbu and Dr. Vinod Scaria. His thesis focused on investigating the genetic epidemiology and genetic variants associated with monogenic dyslipidemia in the Indian population. He has experience in population genomics, handling rare disease patient cohorts, and performing short-read sequencing of these samples. Additionally, he was an active volunteer during the COVID-19 pandemic, working on SARS-CoV-2 genomic surveillance across various states in India. Currently, his research interests lie in building human artificial chromosomes (HACs) for potential clinical applications, and he has further interest in investigating centromere variation too. Apart from his research pursuits, Imran enjoys cooking, trying new cuisines, traveling, and watching movies.
Shenghan Gao, Ph.D.
Postdoctoral fellow
Dr. Shenghan Gao is a postdoctoral fellow in the Logsdon Lab. He completed his Ph.D. at Xi’an Jiaotong University in December 2023 under the supervision of Dr. Kai Ye, where he focused on developing bioinformatics tools to explore chromosome rearrangements and centromere variation in human and plant genomes. Currently, he is working on investigating the variation and evolution of centromeres among the human population and in disease. In his free time, he enjoys playing table tennis, gaming, watching TV dramas, and traveling.
Email: shenghan.gao@pennmedicine.upenn.edu
Pronouns: he/him
Carolina Montaño, MD, PhD, FACMG
T32 fellow & attending physician
Dr. Carolina Montaño is a T32-funded fellow in academic general pediatrics, a clinical and laboratory geneticist, and an Attending Physician in the Division of Human Genetics at the Children's Hospital of Philadelphia (CHOP). After completing her MD/PhD at Johns Hopkins University School of Medicine, she trained in pediatrics at Boston Children's. She then joined the NIH/NHGRI, where she completed both her Clinical Genetics and Genomics residency and Laboratory Genetics and Genomics (LGG) Fellowship, serving as Chief Fellow. Carolina wants to enhance disease diagnosis and uncover mechanisms of disease by integrating ultra-long-read sequencing with comprehensive, deep clinical phenotyping. Originally from Barranquilla, Colombia, Carolina finds peace in spending time with her family (and her Peloton bike), practicing yoga, walking in nature, and learning tai chi.
Pepe
Lab mascot/morale booster
Pepe is a 4-year-old mini goldendoodle who likes to hang out with lab members and visitors. He enjoys cuddles, pets, and treats and is incredibly friendly, social, and loving. By nature, Pepe is hypoallergenic, non-shedding, and fun to be around.
Join us!
The Logsdon lab is hiring at all levels!
Postdoctoral scholars
The Logsdon Lab is looking for talented postdocs to join our team! If you're interested in doing a postdoc in our lab, please email Glennis with a brief statement of your interest, a project you would like to work on, and your CV.
Graduate students
The Logsdon Lab is also recruiting several graduate students! We are affiliated with the following graduate groups/programs at Penn:
If you are interested in rotating in our lab, please email Glennis with a brief statement of your interest and your preferred rotation semester.
Bioinformaticians
We are also recruiting bioinformaticians to work long-read sequencing projects, including the assembly of T2T genomes and the development of software to assess complex repeat regions in diverse genomes. If interested, please email Glennis with a brief statement of your interest, your CV, and contact information of three references.
Lab techs/Long-read sequencing experts
We are looking for lab techs to join our team to perform long-read sequencing on the Oxford Nanopore PromethION. While experience with this technology is preferred, we will also train you to help you develop your skillset. If interested in this position, please email Glennis with a brief statement of your interest, your CV, and contact information of three references.
Undergraduate students
We provide a great training environment for undergraduate students and are supportive of their independence and ability to lead their own project. We offer positions in the summer and year-round. If you're interested in performing research in the lab, please email Glennis with a brief statement of your interest and your CV.
Contact
Glennis Logsdon, Ph.D.
Department of Genetics
Epigenetics Institute
Perelman School of Medicine at the University of Pennsylvania
Email: glogsdon@pennmedicine.upenn.edu
Lab address:
9-176 Smilow Center for Translational Research
3400 Civic Center Blvd.
Philadelphia, PA 19104
Office address:
9-133 Smilow Center for Translational Research
3400 Civic Center Blvd.
Philadelphia, PA 19104