About

Saonli Basu is a Professor in the Division of Biostatistics at the School of Public Health and an Affiliate Professor in the Department of Statistics at the University of Washington. Her research focuses on developing statistical methodologies for genetic mapping of complex traits. She has developed trait-model-free approaches for linkage detection using extended pedigrees and has a broad interest in computational statistics, parametric and nonparametric inferences, and their applications in statistical genetics. Currently, she works on modeling heritability and associations between multiple genetic variants, both rare and common, and single or multiple traits in case-control, cohort, or family studies. Her methodological research is supported by NIH/NIDA R01 and NIH/NIDDK R21 grants, and she is a co-investigator on several R01 projects led by faculty in Epidemiology and Psychology. Her collaborative work addresses statistical issues in pedigree-based or cohort-based genome-wide association studies, applying her methods to diseases such as type 2 diabetes, Alzheimer's, kidney allograft rejection, substance abuse, venous thrombosis, and graft-versus-host disease following hematopoietic stem cell transplant. She is also the co-director of a statistical genomics training grant.

Research topics

• Biology
• Medicine
• Computer Science
• Internal medicine
• Genetics
• Econometrics
• Telecommunications
• Mathematics
• Developmental psychology
• Bioinformatics
• Evolutionary biology
• Oncology
• Statistics
• Demography
• Psychology
• Economics

Selected publications

• Abstract 7892: Multi-ancestry genome-wide association study (GWAS) of pediatric acute myeloid leukemia (AML) risk identifies four risk loci

  Cancer Research · 2026-04-03

  article

  Abstract Introduction: AML is a relatively rare pediatric hematological malignancy, but its treatment outcomes trail other acute leukemias with a 5-year survival rate at ∼70%. While genome-scale susceptibility studies of adult AML risk have been conducted, similar pediatric AML studies have not been published. Methods: 1854 pediatric AML cases (diagnosis age <25y) were assembled from the Children’s Oncology Group (clinical trials AAML-03P1/0531/1031), Hospital for Sick Children (CA), International Berlin-Frankfurt-Münster Study Group (DE), and Royal Alexandra Hospital for Children (AUS). Cases were genotyped with the Illumina HumanOmni 2.5 BeadChip. Using ADMIXTURE-inferred global genetic ancestry, 1355 cases were grouped in African (AFR, N=95), Admixed American (AMR, N=118), East Asian (EAS, N=74) and European (EUR, N=1068) ancestry groups. Sex-/ancestry-matched publicly available adult controls from 3 external cohorts (Age-Related Eye Disease Study, Health and Retirement Study, Long Life Family Study) genotyped with the same platform were identified at a ∼4:1 ratio. TOPMed-based imputation (version r3) supported ancestry-specific GWAS with 5.5-10.7 million common variants (minor allele frequency, MAF≥1%). Logistic regression models adjusted for population substructure tested variant risk associations. Multi-ancestry meta-analysis was performed using an inverse variance-weighted fixed effects model. Results: Four novel genome-wide significant (P<5x10-8) pediatric AML risk loci (PRIM2, HERC2, AGRN, DEFB131A) were identified in the EUR GWAS (N=5340), with moderate per-allele odd ratios (OR range: 1.9-2.9). In silico analyses indicated lead variants at HERC2, AGRN, and DEFB131A loci are in active chromatin regions in blood or bone marrow tissues and overlap transcription factor binding sites, including in leukemia cell lines. The HERC2 index variant (OR=1.9, 95% CI: 1.5-2.3) is associated with HERC2 expression in venous blood (GTEx). Multiple variants at known EUR adult AML risk locus KMT5B were also nominally replicated (P=8.7x10-3). Additional suggestive associations (P<1x10-6) in the AFR (N=475) and AMR (N=518) GWAS were seen; among these, putative pediatric AML risk locus KANK1, which was characterized by low frequency (MAF=1-5%) AFR-specific effect alleles, i.e., nearly absent in other ancestries, is notable for its large risk effects (OR=5.6, 95% CI: 3.0-10.7). The multi-ancestry meta-analysis did not reveal additional genetic signals shared across ancestry groups. Conclusion: We report results from the first pediatric AML GWAS (N=6507, 1355 cases) using international data. We identified 4 novel EUR-specific risk loci, a plausible novel AFR-specific risk locus, and replicated KMT5B, a risk locus reported in a EUR adult AML meta-analysis. Future work includes replication and functional validation studies. Citation Format: Cindy Im, Lauren J. Mills, Peggy Meng, Marijana Vujkovic, Jenny N. Poynter, Melissa Maria Hudson, Kirsten K. Ness, Joseph L. Wiemels, Logan G. Spector, Saonli Basu, Zhaoming Wang, Richard Aplenc. Multi-ancestry genome-wide association study (GWAS) of pediatric acute myeloid leukemia (AML) risk identifies four risk loci [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7892.

  PublisherDOI

• Data from Multiancestry Transcriptome-Wide Association Study Identifies Candidate Genes Associated with Hepatoblastoma

  2025-08-01

  preprintOpen access

  <div>AbstractBackground:<p>Hepatoblastoma (HB) is a rare embryonal liver tumor, with an increasing global incidence that underscores the need to understand its genetic etiology.</p>Methods:<p>Utilizing the ancestry-matched expression quantitative loci data, we performed a HB transcriptome-wide association study (TWAS) on 4,539 Europeans, 1,047 Latinos, and 378 African Americans (∼1:10 case–control ratio). We conducted a meta-analysis of multiancestry transcriptome-wide analysis (METRO), followed by METRO-Egger sensitivity analysis and ancestry-specific gene set enrichment analyses. We further explored genes with additional evidence gathered from independent cohorts and databases.</p>Results:<p>Across the three ancestries, the discovered genes shared the same effect direction across ancestries. A meta-analysis of the three ancestries identified 28 genes significantly associated with HB risk, and 15 were nominally significant for at least two ancestries. Our post-TWAS analyses highlighted 8 genes among these 28, including <i>OXER1</i> (meta-analysis <i>P</i> value = 7.34 × 10<sup>−6</sup>), <i>FADS1</i> (<i>P</i> value = 4.01 × 10<sup>−6</sup>), and <i>UGDH</i> (<i>P</i> value = 5.29 × 10<sup>−8</sup>), which were expressed in fetal liver hepatoblast cells and were differentially expressed in tumor and normal tissues in an independent Japanese HB study (P values = 2.61 × 10<sup>−13</sup>, 3.62 × 10<sup>−3</sup>, and 1.95 × 10<sup>−9</sup>, respectively).</p>Conclusions:<p>We pinpointed eight potential genes associated with HB using data from an ongoing multiancestry genome-wide association study.</p>Impact:<p>We conducted the largest HB TWAS to date, prompting further exploration of genes.</p></div>

  PublisherDOI

• Figure S9 from Multiancestry Transcriptome-Wide Association Study Identifies Candidate Genes Associated with Hepatoblastoma

  2025-08-01

  preprintOpen access

  <p>Plotted differential expression of normalized gene counts for the top 6 down-regulated genes by Log2 fold changes (LFC) for the Japanese HB cohort.</p>

  PublisherDOI

• Figure S10 from Multiancestry Transcriptome-Wide Association Study Identifies Candidate Genes Associated with Hepatoblastoma

  2025-08-01

  preprintOpen access

  <p>Normal liver vs. HB tumor differential gene expression analyses.</p>

  PublisherDOI

• Examining the heritability of functional brain networks in adolescence

  Research Square · 2025-10-31

  preprintOpen access
  PublisherOA PDFDOI

• Figure S8 from Multiancestry Transcriptome-Wide Association Study Identifies Candidate Genes Associated with Hepatoblastoma

  2025-08-01

  preprintOpen access

  <p>Plotted differential expression of normalized gene counts for the top 6 up-regulated genes by Log2 fold changes (LFC) for the Japanese HB cohort.</p>

  PublisherDOI

• Figure S3 from Multiancestry Transcriptome-Wide Association Study Identifies Candidate Genes Associated with Hepatoblastoma

  2025-08-01

  preprintOpen access

  <p>Manhattan plots of METRO-Egger analysis at 250kb</p>

  PublisherDOI

• Impact of Maternal Iron Deficiency in Early Pregnancy on Neonatal Iron Status and Neurodevelopment at Two Years of Age: a Prospective, Maternal-Infant Cohort Study

  Journal of Nutrition · 2025-11-14 · 4 citations

  articleOpen access

  BACKGROUND: Iron deficiency during pregnancy has potentially serious health consequences for both the mother and her offspring. Few prospective studies have considered the impact of maternal nonanemic iron deficiency in early pregnancy on offspring health outcomes. OBJECTIVE: The objective of this study was to explore the impact of maternal iron deficiency in early pregnancy on neonatal iron status at birth and neurodevelopment at 2 y of age. METHODS: In a low-risk, primiparous nonanemic maternal-infant cohort, ferritin, soluble transferrin receptors, and inflammatory markers (C-reactive protein and α-glycoprotein) were measured at 15- and 20-weeks of gestation and in umbilical cord blood. Bayley Scales of Infant and Toddler Development (BSID-III) and the Child Behavior Checklist were assessed at 2 y. RESULTS: Participants with complete longitudinal data from 15 weeks of gestation to 2 y (n = 189) were Caucasian (96.8%), highly educated (78.8% university graduates), with singleton pregnancies. At 15-weeks of gestation, 3.2% had ferritin <15 μg/L and 18.5% had ferritin <30 μg/L, which increased to 8.5% and 42.3% <15 and <30 μg/L, respectively, at 20-weeks. Iron depletion (cord ferritin <76 μg/L) was observed in 7.4% of newborn infants. Cord ferritin concentrations were 42.3 μg/L lower in infants born to iron deficient mothers (using maternal ferritin <30 μg/L threshold) at 15-weeks, compared with those with iron sufficient mothers. Children born to mothers with ferritin <30 μg/L at 15- and 20-wk had lower BSID-III language [Estimated β (95% confidence interval), 15-wk: -7.3 (-14.0, -0.4), 20-wk: -6.3 (-11.0, -1.3)] and motor [15-wk: -5.8 (-11.0, -1.1), 20-wk: -4.0 (-7.8, -0.3)] composite scores at 2 y than those with iron sufficient mothers. CONCLUSIONS: Maternal nonanemic iron deficiency in early pregnancy was associated with low iron status at birth and worse language and motor outcomes at 2 y of age. This new evidence highlights the need to consider screening for iron deficiency early in pregnancy, even in well-resourced settings. This trial was registered at clinicaltrials.gov as NCT01891240.

  PublisherDOI

• Genome-wide association study of childhood B-cell acute lymphoblastic leukemia reveals novel African ancestry-specific susceptibility loci

  Nature Communications · 2025-10-22 · 1 citations

  articleOpen access

  Abstract B-cell acute lymphoblastic leukemia (B-ALL) is the most common pediatric malignancy. Given racial/ethnic differences in incidence and outcomes, B-ALL genome-wide association studies among children of African ancestry are needed. Leveraging multi-institutional datasets with 840 African American children with B-ALL and 3360 controls, nine loci achieved genome-wide significance ( P &lt; 5 × 10 −8 ) after meta-analysis. Two loci were established trans-ancestral susceptibility regions ( IKZF1 , ARID5B ), while the remaining novel loci were specific to African populations. Five-year overall survival among children carrying novel risk alleles was significantly worse (83% versus 96% in non-carriers, P = 4.8 × 10 −3 ). Novel risk variants were also associated with subtype-specific disease ( P &lt; 0.05), including higher susceptibility for a subtype overrepresented in African American children ( TCF3-PBX1 ) and lower susceptibility for a subtype with excellent prognosis ( ETV6-RUNX1 ). Functional experiments revealed novel B-ALL risk variants had allele-specific differences in transcriptional activity ( P &lt; 0.05) in B-cell and leukemia cell lines. These findings shed insights into ancestry-related differences in leukemogenesis and prognosis.

  PublisherOA PDFDOI

• Figure S2 from Multiancestry Transcriptome-Wide Association Study Identifies Candidate Genes Associated with Hepatoblastoma

  2025-08-01

  preprintOpen access

  &lt;p&gt;Plots comparing the effect of imputed gene expression on hepatoblastoma risk by METRO and METRO-Egger Analysis (250kb)&lt;/p&gt;

  PublisherDOI

Recent grants

• NIH Grant R01DA033958

  NIH · $823k · 2020

• Improved Heritability Estimation by Spatial Mapping of Genetic Relationships

  NIH · $218k · 2018–2020

• NIH Grant R01DA03395802

  NIH · $277k · 2017

• Improved Heritability Estimation by Spatial Mapping of Genetic Relationships

  NIH · $180k · 2018–2023

• NIH Grant R21DK089351

  NIH · $394k · 2014

Frequent coauthors

• David‐Alexandre Trégouët

  Université de Bordeaux

  61 shared

• Nicholas L. Smith

  VA Puget Sound Health Care System

  59 shared

• Pierre‐Emmanuel Morange

  Aix-Marseille Université

  58 shared

• Aaron R. Folsom

  University of Minnesota

  44 shared

• Daniel I. Chasman

  42 shared

• Philippe Amouyel

  Université de Lille

  41 shared

• David M. Smadja

  Assistance Publique – Hôpitaux de Paris

  37 shared

• James S. Pankow

  University of Minnesota

  37 shared

Education

• PhD, Statistics

  University of Washington

Awards & honors

• Member, Delta Omega Honorary Society in Public Health
• American Statistical Association
• International Biometric Society
• International Genetic Epidemiology Society
• Caucus for Women in Statistics