Santhosh Girirajan

Professor of Genomics; Professor of Anthropology; Department Head of Biochemistry and Molecular Biology

Santhosh Girirajan

Research Summary

Understanding the genetic basis of neurodevelopmental disorders.

Huck Graduate Students

Huck Affiliations

Links

Most Recent Publications

Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism

Soo Whee Kim, Hyeji Lee, Da Yea Song, Gang Hee Lee, Jungeun Ji, Jung Woo Park, Jae Hyun Han, Jee Won Lee, Hee Jung Byun, Ji Hyun Son, Ye Rim Kim, Yoojeong Lee, Jaewon Kim, Ashish Jung, Junehawk Lee, Eunha Kim, So Hyun Kim, Jeong Ho Lee, F. Kyle Satterstrom, Santhosh Girirajan, Anders D. Børglum, Jakob Grove, Eunjoon Kim, Donna M. Werling, Hee Jeong Yoo, Joon Yong An, 2024, Genome Medicine

Flynotyper 2.0: an updated tool for rapid quantitative assessment of Drosophila eye phenotypes

Johnathan Ray, Deepro Banerjee, Qingyu Wang, Santhosh Girirajan, 2024, G3: Genes, Genomes, Genetics

Strategies for dissecting the complexity of neurodevelopmental disorders

Jiawan Sun, Serena Noss, Deepro Banerjee, Maitreya Das, Santhosh Girirajan, 2024, Trends in Genetics on p. 187-202

Transcriptome signatures of the medial prefrontal cortex underlying GABAergic control of resilience to chronic stress exposure

Meiyu Shao, Julia Botvinov, Deepro Banerjee, Santhosh Girirajan, Bernhard Lüscher, 2024, Molecular Psychiatry on p. 2197-2209

Assortative mating and parental genetic relatedness contribute to the pathogenicity of variably expressive variants

Corrine Smolen, Matthew Jensen, Lisa Dyer, Lucilla Pizzo, Anastasia Tyryshkina, Deepro Banerjee, Laura Rohan, Emily Huber, Laila El Khattabi, Paolo Prontera, Jean Hubert Caberg, Anke Van Dijck, Charles Schwartz, Laurence Faivre, Patrick Callier, Anne Laure Mosca-Boidron, Mathilde Lefebvre, Kate Pope, Penny Snell, Paul J. Lockhart, Lucia Castiglia, Ornella Galesi, Emanuela Avola, Teresa Mattina, Marco Fichera, Giuseppa Maria Luana Mandarà, Maria Grazia Bruccheri, Olivier Pichon, Cedric Le Caignec, Radka Stoeva, Silvestre Cuinat, Sandra Mercier, Claire Bénéteau, Sophie Blesson, Ashley Nordsletten, Dominique Martin-Coignard, Erik Sistermans, R. Frank Kooy, David J. Amor, Corrado Romano, Bertrand Isidor, Jane Juusola, Santhosh Girirajan, 2023, American Journal of Human Genetics on p. 2015-2028

Challenges and considerations for reproducibility of STARR-seq assays

Maitreya Das, Ayaan Hossain, Deepro Banerjee, Craig Alan Praul, Santhosh Girirajan, 2023, Genome Research on p. 479-495

Genome-wide analysis of copy-number variation in humans with cleft lip and/or cleft palate identifies COBLL1, RIC1, and ARHGEF38 as clefting genes

Lisa A. Lansdon, Amanda Dickinson, Sydney Arlis, Huan Liu, Arman Hlas, Alyssa Hahn, Greg Bonde, Abby Long, Jennifer Standley, Anastasia Tyryshkina, George Wehby, Nanette R. Lee, Sandra Daack-Hirsch, Karen Mohlke, Santhosh Girirajan, Benjamin W. Darbro, Robert A. Cornell, Douglas W. Houston, Jeffrey C. Murray, J. Robert Manak, 2023, American Journal of Human Genetics on p. 71-91

Pathogenic Variants and Ascertainment: Neuropsychiatric Disease Risk in a Health System Cohort

Deepro Banerjee, Santhosh Girirajan, 2023, American Journal of Psychiatry on p. 11-13

Artificial gravity partially protects space-induced neurological deficits in Drosophila melanogaster

Siddhita D. Mhatre, Janani Iyer, Juli Petereit, Roberta M. Dolling-Boreham, Anastasia Tyryshkina, Amber M. Paul, Rachel Gilbert, Matthew Jensen, Rebekah J. Woolsey, Sulekha Anand, Marianne B. Sowa, David R. Quilici, Sylvain V. Costes, Santhosh Girirajan, Sharmila Bhattacharya, 2022, Cell Reports

The gene dose makes the disease

Corrine Smolen, Santhosh Girirajan, 2022, Cell on p. 2850-2852

Most-Cited Papers

Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants

Lucilla Pizzo, Matthew Jensen, Andrew Polyak, Jill A. Rosenfeld, Katrin Mannik, Arjun Krishnan, Elizabeth McCready, Olivier Pichon, Cedric Le Caignec, Anke Van Dijck, Kate Pope, Els Voorhoeve, Jieun Yoon, Paweł Stankiewicz, Sau Wai Cheung, Damian Pazuchanics, Emily Huber, Vijay Kumar, Rachel L. Kember, Francesca Mari, Aurora Curró, Lucia Castiglia, Ornella Galesi, Emanuela Avola, Teresa Mattina, Marco Fichera, Luana Mandarà, Marie Vincent, Mathilde Nizon, Sandra Mercier, Claire Bénéteau, Sophie Blesson, Dominique Martin-Coignard, Anne Laure Mosca-Boidron, Jean Hubert Caberg, Maja Bucan, Susan Zeesman, Małgorzata J.M. Nowaczyk, Mathilde Lefebvre, Laurence Faivre, Patrick Callier, Cindy Skinner, Boris Keren, Charles Perrine, Paolo Prontera, Nathalie Marle, Alessandra Renieri, Alexandre Reymond, R. Frank Kooy, Bertrand Isidor, Charles Schwartz, Corrado Romano, Erik Sistermans, David J. Amor, Joris Andrieux, Santhosh Girirajan, 2019, Genetics in Medicine on p. 816-825

R47H variant of TREM2 associated with Alzheimer disease in a large late-onset family clinical, genetic, and neuropathological study

Olena Korvatska, James B. Leverenz, Suman Jayadev, Pamela McMillan, Irina Kurtz, Xindi Guo, Malia Rumbaugh, Mark Matsushita, Santhosh Girirajan, Michael O. Dorschner, Kostantin Kiianitsa, Chang En Yu, Zoran Brkanac, Gwenn A. Garden, Wendy H. Raskind, Thomas D. Bird, 2015, JAMA Neurology on p. 920-927

Comorbidity of intellectual disability confounds ascertainment of autism: Implications for genetic diagnosis

Andrew Polyak, Richard M. Kubina, Santhosh Girirajan, 2015, American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics on p. 600-608

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects

James R. Priest, Kazutoyo Osoegawa, Nebil Mohammed, Vivek Nanda, Ramendra Kundu, Kathleen Schultz, Edward J. Lammer, Santhosh Girirajan, Todd Scheetz, Daryl Waggott, Francois Haddad, Sushma Reddy, Daniel Bernstein, Trudy Burns, Jeffrey D. Steimle, Xinan H. Yang, Ivan P. Moskowitz, Matthew Hurles, Richard P. Lifton, Debbie Nickerson, Michael Bamshad, Evan E. Eichler, Seema Mital, Val Sheffield, Thomas Quertermous, Bruce D. Gelb, Michael Portman, Euan A. Ashley, 2016, PLoS Genetics on p. e1005963

An assessment of sex bias in neurodevelopmental disorders

Andrew Polyak, Jill A. Rosenfeld, Santhosh Girirajan, 2015, Genome Medicine

Epigenetics of autism-related impairment: Copy number variation and maternal infection

Varvara Mazina, Jennifer Gerdts, Sandy Trinh, Katy Ankenman, Tracey Ward, Megan Y. Dennis, Santhosh Girirajan, Evan E. Eichler, Raphael Bernier, 2015, Journal of Developmental and Behavioral Pediatrics on p. 61-67

Quantitative assessment of eye phenotypes for functional genetic studies using Drosophila melanogaster

Janani Iyer, Qingyu Wang, Thanh Le, Lucilla Pizzo, Sebastian Grönke, Surendra S. Ambegaokar, Yuzuru Imai, Ashutosh Srivastava, Beatriz Llamusí Troisí, Graeme Mardon, Ruben Artero, George R. Jackson, Adrian M. Isaacs, Linda Partridge, Bingwei Lu, Justin P. Kumar, Santhosh Girirajan, 2016, G3: Genes, Genomes, Genetics on p. 1427-1437

Parental Origin of Interstitial Duplications at 15q11.2-q13.3 in Schizophrenia and Neurodevelopmental Disorders

Anthony R. Isles, Andrés Ingason, Chelsea Lowther, James Walters, Micha Gawlick, Gerald Stöber, Elliott Rees, Joanna Martin, Rosie B. Little, Harry Potter, Lyudmila Georgieva, Lucilla Pizzo, Norio Ozaki, Branko Aleksic, Itaru Kushima, Masashi Ikeda, Nakao Iwata, Douglas F. Levinson, Pablo V. Gejman, Jianxin Shi, Alan R. Sanders, Jubao Duan, Joseph Willis, Sanjay Sisodiya, Gregory Costain, Thomas M. Werge, Franziska Degenhardt, Ina Giegling, Dan Rujescu, Stefan J. Hreidarsson, Evald Saemundsen, Joo Wook Ahn, Caroline Ogilvie, Santhosh D. Girirajan, Hreinn Stefansson, Kari Stefansson, Michael C. O’Donovan, Michael J. Owen, Anne Bassett, George Kirov, 2016, PLoS Genetics

Pervasive genetic interactions modulate neurodevelopmental defects of the autism-Associated 16p11.2 deletion in Drosophila melanogaster

Janani Iyer, Mayanglambam Dhruba Singh, Matthew Jensen, Payal Patel, Lucilla Pizzo, Emily Huber, Haley Koerselman, Alexis T. Weiner, Paola Lepanto, Komal Vadodaria, Alexis Kubina, Qingyu Wang, Abigail Talbert, Sneha Yennawar, Jose Badano, J. Robert Manak, Melissa M. Rolls, Arjun Krishnan, Santhosh Girirajan, 2018, Nature Communications

Novel metrics to measure coverage in whole exome sequencing datasets reveal local and global non-uniformity

Qingyu Wang, Cooduvalli S. Shashikant, Matthew Jensen, Naomi S. Altman, Santhosh Girirajan, 2017, Scientific Reports

News Articles Featuring Santhosh Girirajan

Jul 14, 2025

The breadth of the brain

Researchers in the Penn State Neuroscience Institute study the brain’s many aspects in a variety of ways, with implications from mental health to aging and disease.

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Jan 23, 2025

$17.9M NIH grant to research neurodevelopment disorders

Illuminating key biological pathways that underlie neurodevelopmental and psychiatric disorders, such as autism spectrum disorder and attention deficit hyperactivity disorder, is the goal of a new five-year, $17.9 million grant from the National Institutes of Health’s National Institute of Mental Health to a national team of researchers.

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Dec 16, 2024

Brain regions that relieve effects of chronic stress in mice differ based on sex

In two new studies, researchers made mice resilient to stress by activating neurons in different brain regions and found that the changes involved are highly sex-specific

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Oct 09, 2024

Potential breakthrough as experts discover factor during pregnancy they think causes autism

Scientists have grappled with the puzzle of autism's origins for decades - now a study suggests a bad cold or flu during pregnancy could be a cause.

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Aug 22, 2024

What is a nonverbal learning disorder? Tim Walz’s son Gus’ condition, explained

Almost 3 million kids in North America have the learning disability NVLD. It affects spatial-visual skills and has nothing to do with speaking abilities.

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Apr 23, 2024

Penn State molecular biologist Ross Hardison named an AAAS Fellow

Ross Hardison, Academy Professor and professor emeritus of biochemistry and molecular biology, has been named a fellow of the American Association for the Advancement of Science (AAAS).

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Feb 14, 2024

Penn State molecular biologist Joseph Reese named distinguished professor

Joseph Reese, professor of biochemistry and molecular biology, has been selected to receive the title of Distinguished Professor of Biochemistry and Molecular Biology

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Feb 07, 2024

Parental Traits May Influence Neurodevelopmental Disorders

Researchers revealed that evaluating parental traits for neurodevelopmental and psychiatric disorders offers a more precise prediction for these conditions in children than genetic testing alone

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Feb 07, 2024

Predicting neurodevelopmental disease in children from parent’s traits

Predicting the trajectory of neurodevelopmental and psychiatric disorders like autism or schizophrenia is difficult because they can be influenced by many different genetic and environmental factors

Full Article

Jan 15, 2024

Honors for Booker, Girirajan, Llinás

3 Penn State researchers have received awards and new titles

Full Article

Oct 03, 2023

Girirajan named T. Ming Chu Professor of Biochemistry and Molecular Biology

Santhosh Girirajan, professor and interim head of the Penn State Department of Biochemistry and Molecular Biology, has been named the T. Ming Chu Professor of Biochemistry and Molecular Biology.

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Jul 06, 2023

Partner selection may amplify rare variants in children

Partners who share similar traits of a given condition, such as autism, may concentrate rare genetic variants in their children, increasing the likelihood of having a child with that condition, according to a new preprint.

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Jun 12, 2023

Penn State announces tenure-line faculty promotions, effective July 1, 2023

The following is a list of academic promotions for tenured and tenure-line faculty members at Penn State, effective July 1, 2023.

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May 18, 2023

Genetic background sways effects of autism-linked mutation

An autism-linked mutation disrupts the development of clusters of brain cells, or brain organoids, generated from autistic people but displays significantly less of an effect in organoids produced from neurotypical donors, a new study finds.

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Apr 19, 2023

U.S. study charts changing prevalence of profound and non-profound autism

More than a quarter of autistic 8-year-olds in the United States have profound autism, according to a study published today in Public Health Reports. Although the overall prevalence of profound autism in this age group increased from 2002 to 2016, the prevalence of non-profound autism did so at a sharper rate, the findings show.

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Jan 26, 2023

Autism rates have tripled. Is it now more common or are we just better at diagnosis?

Autism rates tripled among children in the New York and New Jersey metropolitan area from 2000 to 2016, according to a study published Thursday in the journal Pediatrics.

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Jan 26, 2023

Autism rates have tripled. Is it now more common or are we just better at diagnosis?

New research suggests doctors have improved at identifying autism, especially among children with average or above-average IQs. But that doesn't fully explain the trend.

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Jun 24, 2020

Genes affecting brains and brawn?

Genes located in "copy number variants" (CNVs) — parts of chromosomes that are missing in some individuals and duplicated in others — that are associated with neurodevelopmental disorders affect more than just brain development, according to new research..

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Sep 26, 2019

Apparent new rise in autism may not reflect true prevalence

New statistics on autism prevalence in the United States suggest a dramatic rise in the number of children with the condition. But it is unlikely that these numbers reflect a true rise in prevalence, experts say.

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Aug 19, 2019

Researchers Create Mini Livers To Test Disease Progression

Scientists have bioengineered miniature human livers – possibly for the first time. The livers were created by University of Pittsburgh researchers in an effort to move away from less reliable experiments on mouse livers.

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Aug 19, 2019

Pa. researchers create mini livers to test disease progression

Scientists have bioengineered miniature human livers - possibly for the first time. The livers were created by University of Pittsburgh researchers in an effort to move away from less reliable experiments on mouse livers.

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Jul 30, 2019

Bioinformatics and Genomics Student Inspires Journal Cover

The July 2019 issue of Genome Research features art inspired by the work of Penn State graduate student Vijay Kumar Pounraja.

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Jul 09, 2019

New method helping to find deletions and duplications in the human genome

A new machine-learning method accurately identifies regions of the human genome that have been duplicated or deleted — known as copy number variants — that are often associated with autism and other neurodevelopmental disorders. The new method, developed by researchers at Penn State, integrates data from several algorithms that attempt to identify copy number variants from exome-sequencing data — high-throughput DNA sequencing of only the protein-coding regions of the human genome.

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Sep 19, 2018

Family's 'Genetic Background' Sheds Light On Autism Symptoms

The total amount of rare mutations—deletions, duplications, or other changes to the DNA sequence—in a person’s genome can explain why individuals with a disease-associated mutation can have vastly different symptoms, according to new research.

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Sep 10, 2018

Family Genetics Key to Severity of Autism and Other Neurodevelopmental Disorders

A major international research effort headed by a team at the Pennsylvania State University now reports study data indicating that while the primary risk variant may make an individual more susceptible to developing a particular disorder, such as ASD, the variability and severity of symptoms will depend on their genetic background of accumulated rare mutations—such as deletions and duplications—which have been inherited from parents and grandparents.

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