4.7 Review

Systems pharmacology and genome medicine: a future perspective

Journal

GENOME MEDICINE
Volume 1, Issue -, Pages -

Publisher

BIOMED CENTRAL LTD
DOI: 10.1186/gm11

Keywords

-

Funding

  1. NIH [GM54508]
  2. New York Systems Biology Center [P50-GM071558]
  3. predoctoral training grant in Pharmacological Sciences [GM-062754]
  4. NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM054508] Funding Source: NIH RePORTER

Ask authors/readers for more resources

Genome medicine uses genomic information in the diagnosis of disease and in prescribing treatment. This transdisciplinary field brings together knowledge on the relationships between genetics, pathophysiology and pharmacology. Systems pharmacology aims to understand the actions and adverse effects of drugs by considering targets in the context of the biological networks in which they exist. Genome medicine forms the base on which systems pharmacology can develop. Experimental and computational approaches enable systems pharmacology to obtain holistic, mechanistic information on disease networks and drug responses, and to identify new drug targets and specific drug combinations. Network analyses of interactions involved in pathophysiology and drug response across various scales of organization, from molecular to organismal, will allow the integration of the systems-level understanding of drug action with genome medicine. The interface of the two fields will enable drug discovery for personalized medicine. Here we provide a perspective on the questions and approaches that drive the development of these new interrelated fields.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.7
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Review Endocrinology & Metabolism

Nonimmune hydrops fetalis and congenital disorders of glycosylation: A systematic literature review

Mona M. Makhamreh, Naiga Cottingham, Carlos R. Ferreira, Seth Berger, Huda B. Al-Kouatly

JOURNAL OF INHERITED METABOLIC DISEASE (2020)

Article Genetics & Heredity

Loss-of-Function Variants in PPP1R12A: From Isolated Sex Reversal to Holoprosencephaly Spectrum and Urogenital Malformations

Joel J. Hughes, Ebba Alkhunaizi, Paul Kruszka, Louise C. Pyle, Dorothy K. Grange, Seth I. Berger, Katelyn K. Payne, Diane Masser-Frye, Tommy Hu, Michelle R. Christie, Nancy J. Clegg, Joshua L. Everson, Ariel F. Martinez, Laurence E. Walsh, Emma Bedoukian, Marilyn C. Jones, Catharine Jean Harris, Korbinian M. Riedhammer, Daniela Choukair, Patricia Y. Fechner, Meilan M. Rutter, Sophia B. Hufnagel, Maian Roifman, Gad B. Kletter, Emmanuele Delot, Eric Vilain, Robert J. Lipinski, Chad M. Vezina, Maximilian Muenke, David Chitayat

AMERICAN JOURNAL OF HUMAN GENETICS (2020)

Article Genetics & Heredity

Rapid deployment of a telemedicine care model for genetics and metabolism duringCOVID-19

Natasha Shur, Shireen M. Atabaki, Monisha S. Kisling, Abir Tabarani, Clarence Williams, Jamie L. Fraser, Debra S. Regier, Marshall Summar

Summary: Telemedicine has played a crucial role in the current COVID-19 pandemic, emphasizing the importance of safe and effective patient care. The program, focusing on patient's homes, aimed to increase access to care, reduce missed work, and improve scheduling by conducting visits through physician medical geneticists, genetic counselors, and biochemical dietitians. This pilot-program successfully optimized patient safety and workforce preservation, providing full access to patients during the pandemic and proving the effectiveness and value of telemedicine for a complex medical population.

AMERICAN JOURNAL OF MEDICAL GENETICS PART A (2021)

Review Genetics & Heredity

A systematic review of monogenic etiologies of nonimmune hydrops fetalis

Andrea M. Quinn, Breanna N. Valcarcel, Mona M. Makhamreh, Huda B. Al-Kouatly, Seth I. Berger

Summary: Hydrops fetalis (HF) is a life-threatening condition caused by fluid accumulation in fetal compartments, with genetic causes including chromosomal and monogenic disorders. Current clinical workup often does not fully evaluate genetic targets, leading to a need for broader molecular testing. Research identifies numerous genes associated with nonimmune HF, some with emerging evidence, suggesting potential treatment implications. Broad sequencing approaches like exome sequencing may be useful in improving clinical management of HF.

GENETICS IN MEDICINE (2021)

Article Cardiac & Cardiovascular Systems

Exome Sequencing and Congenital Heart Disease in Sub-Saharan Africa

Ekanem N. Ekure, Adebowale Adeyemo, Hanhan Liu, Ogochukwu Sokunbi, Nnenna Kalu, Ariel F. Martinez, Babajide Owosela, Cedrik Tekendo-Ngongang, Yonit A. Addissie, Akinsanya Olusegun-Joseph, Desmond Ikebudu, Seth Berger, Maximilian Muenke, Zhe Han, Paul Kruszka

Summary: This study identified novel candidate genes and variants for CHD through exome sequencing, facilitating comparisons with previous studies in predominantly European cohorts. It represents an important first step in genomic studies of CHD in understudied populations.

CIRCULATION-GENOMIC AND PRECISION MEDICINE (2021)

Article Genetics & Heredity

High diagnosis rate for nonimmune hydrops fetalis with prenatal clinical exome from the Hydrops-Yielding Diagnostic Results of Prenatal Sequencing (HYDROPS) Study

Huda B. Al-Kouatly, Mona M. Makhamreh, Stephanie M. Rice, Kelsey Smith, Christopher Harman, Andrea Quinn, Breanna N. Valcarcel, Brandy Firman, Ruby Liu, Madhuri Hegde, Elizabeth Critchlow, Seth I. Berger

Summary: Testing with prenatal exome sequencing (ES) for nonimmune hydrops fetalis (NIHF) after negative standard workup can yield 50% diagnostic results and may provide crucial information for postnatal prognosis and future pregnancies.

GENETICS IN MEDICINE (2021)

Article Genetics & Heredity

Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder

Sebastien Kury, Frederic Ebstein, Alice Molle, Thomas Besnard, Ming-Kang Lee, Virginie Vignard, Tiphaine Hery, Mathilde Nizon, Grazia M. S. Mancini, Jacques C. Giltay, Benjamin Cogne, Kirsty McWalter, Wallid Deb, Hagar Mor-Shaked, Hong Li, Rhonda E. Schnur, Ingrid M. Wentzensen, Anne-Sophie Denomme-Pichon, Cynthia Fourgeux, Frans W. Verheijen, Eva Faurie, Rachel Schot, Cathy A. Stevens, Daphne J. Smits, Eileen Barr, Ruth Sheffer, Jonathan A. Bernstein, Chandler L. Stimach, Eliana Kovitch, Vandana Shashi, Kelly Schoch, Whitney Smith, Richard H. van Jaarsveld, Anna C. E. Hurst, Kirstin Smith, Evan H. Baugh, Suzanne G. Bohm, Emilie Vyhnalkova, Lukas Ryba, Capucine Delnatte, Juanita Neira, Dominique Bonneau, Annick Toutain, Jill A. Rosenfeld, Severine Audebert-Bellanger, Brigitte Gilbert-Dussardier, Sylvie Odent, Frederic Laumonnier, Seth Berger, Ann C. M. Smith, Franck Bourdeaut, Marc-Henri Stern, Richard Redon, Elke Krueger, Raphael Margueron, Stephane Bezieau, Jeremie Poschmann, Bertrand Isidor

Summary: This study reports on a rare syndromic neurodevelopmental disorder caused by rare germline missense BAP1 variants, and provides evidence that these variants alter chromatin remodeling and transcriptional dysregulation of developmental genes.

AMERICAN JOURNAL OF HUMAN GENETICS (2022)

Review Obstetrics & Gynecology

Etiology and Outcome of Isolated Fetal Ascites A Systematic Review

Rebecca Horgan, Julia A. Youssef, Ariel T. Levy, Seth Berger, Sophie Dreux, Maria L. Brizot, Alison Boutall, Alfred Z. Abuhamad, Ana M. Angarita, Huda B. Al-Kouatly

Summary: Isolated fetal ascites has diverse etiologies, with survival rates related to the underlying cause. In most cases, fetal ascites does not progress to fetal hydrops.

OBSTETRICS AND GYNECOLOGY (2021)

Article Pediatrics

Recessive GCH1 Deficiency Causing DOPA-Responsive Dystonia Diagnosed by Reported Negative Exome

Seth I. Berger, Ilana Miller, Laura Tochen

Summary: This study reported a case of a child who initially had negative results on whole exome sequencing, but further evaluation and analysis led to a diagnosis of treatable DOPA-responsive dystonia. It highlights the importance of careful review of uncertain variants and consideration of the clinical context during exome sequencing.

PEDIATRICS (2022)

Article Cell & Tissue Engineering

A library of induced pluripotent stem cells from clinically well-characterized, diverse healthy human individuals

Christoph Schaniel, Priyanka Dhanan, Bin Hu, Yuguang Xiong, Teeya Raghunandan, David M. Gonzalez, Rafael Dariolli, Sunita L. D'Souza, Arjun S. Yadaw, Jens Hansen, Gomathi Jayaraman, Bino Mathew, Moara Machado, Seth I. Berger, Joseph Tripodi, Vesna Najfeld, Jalaj Garg, Marc Miller, Colleen S. Surlyn, Katherine C. Michelis, Neelima C. Tangirala, Himali Weerahandi, David C. Thomas, Kristin G. Beaumont, Robert Sebra, Milind Mahajan, Eric Schadt, Dusica Vidovic, Stephan C. Schurer, Joseph Goldfarb, Evren U. Azeloglu, Marc R. Birtwistle, Eric A. Sobie, Jason C. Kovacic, Nicole C. Dubois, Ravi Iyengar

Summary: The library of hiPSC lines from clinically healthy human subjects is a valuable resource for various studies on human biology. These hiPSC lines are well-characterized, gender-balanced, and racially/ethnically diverse, ranging in age from 22 to 61 years. The extensive characterization of the hiPSC lines includes whole-genome sequencing data, genomic ancestry determination, and analysis of mendelian disease genes and risks.

STEM CELL REPORTS (2021)

Article Genetics & Heredity

Genomic and biochemical analysis of repeatedly observed variants in DBT in individuals with maple syrup urine disease of Central American ancestry

Charles J. Billington, Kimberly A. Chapman, Eyby Leon, Beatrix W. Meltzer, Seth Berger, Matthew Olson, Robert A. Figler, Steve A. Hoang, Cui Wanxing, Brian R. Wamhoff, M. Sol Collado, Kristina Cusmano-Ozog

Summary: Maple syrup urine disease (MSUD) is a genetic metabolic disorder characterized by hyperleucinemia, brain swelling, and death. In this case series, patients with MSUD caused by DBT gene mutations were studied. These mutations led to decreased protein production and accumulation of branched-chain amino acids and alpha-ketoacids. The patients presented with classical MSUD with neonatal onset and were all from families who immigrated from Honduras or El Salvador.

AMERICAN JOURNAL OF MEDICAL GENETICS PART A (2022)

Article Endocrinology & Metabolism

Fetal pharmacogenomics: A promising addition to complex neonatal care

Megan Raymond, Elizabeth Critchlow, Stephanie M. Rice, Sascha Wodoslawsky, Seth I. Berger, Madhuri Hegde, Philip E. Empey, Huda B. Al-Kouatly

Summary: This study assessed parental desire for PGx testing and found that the majority of parents were interested in receiving PGx results. Furthermore, it revealed that 89% of the tested individuals had actionable PGx variants. The feasibility of obtaining fetal PGx data for medically complex neonates was also demonstrated.

MOLECULAR GENETICS AND METABOLISM (2022)

Meeting Abstract Obstetrics & Gynecology

Hydrops-Yielding Diagnostic Results Of Prenatal Exome Sequencing (HYDROPS) Trial - Prenatal WES for NIHF

Huda B. Al-Kouatly, Mona M. Makhamreh, Stephanie M. Rice, Kelsey Smith, Christopher Harman, Andrea Quinn, Breanna Valcarcel, Brandy Firman, Ruby Liu, Madhuri Hedge, Elizabeth Critchlow, Seth I. Berger

AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY (2021)

Meeting Abstract Obstetrics & Gynecology

Pregnancy Outcomes in Women With Acute Porphyria: A Systematic Literature Review

Tomi T. Kanninen, Emily Stroobant, Rebecca Pierce-Williams, Seth Berger, Huda B. Al-Kouatly

OBSTETRICS AND GYNECOLOGY (2020)

Meeting Abstract Genetics & Heredity

PPP1R12A IS ASSOCIATED WITH HOLOPROSENCEPHALY SPECTRUM BRAIN

J. Hughes, P. Kruszka, S. I. Berger, K. Payne, D. Masser-Frye, T. Hu, J. L. Everson, A. F. Martinez, L. Walsh, M. Jones, R. J. Lipinski, M. Muenke

AMERICAN JOURNAL OF MEDICAL GENETICS PART A (2020)

No Data Available