Few shot learning for phenotype-driven diagnosis of patients with rare genetic diseases

Emily Alsentzer et al.

Using real-world cohorts from the Undiagnosed Diseases Network, SHEPHERD—a few-shot learning approach for multi-faceted rare disease diagnosis—was assessed. Deep phenotyping of the 465 UDN patients was performed by PhenoTips, a tool integrated into the electronic health record that allows for structured phenotyping of patient symptoms.

NATURE PARTNERS JOURNAL.

JUN 20, 2025

Singleton rapid long-read genome sequencing as first tier genetic test for critically Ill children with suspected genetic diseases

Wuttichart Kamolvisit et al.

The benefits of singleton rapid long-read genome sequencing (rLR-GS) at two tertiary hospitals in Thailand were explored for critically ill children admitted to ICU with a suspected genetic etiology. PhenoTips software was used for collaboration to ensure efficient communication between clinical teams and laboratories.

EUROPEAN JOURNAL OF HUMAN GENETICS.

FEB 27, 2025

A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery

The multi-coloured logo of the Global Alliance for Genomics and Health. GA4GH.

Daniel Danis et al.

The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema a standard for sharing clinical and genomic information about an individual that can facilitate phenotype-driven genomic diagnostics, patient classification, and stratification. PhenoTips was used as a tool for upstream data collection and management and supported exporting patient profiles as phenopackets for downstream analysis and data sharing.

HUMAN GENETICS AND GENOMICS ADVANCES.

JAN 9, 2025

Genomic Answers for Kids: Toward more equitable access to genomic testing for rare diseases in rural populations

Children's Mercy Kansas City logo in blue next to a blue outline of an adult figure holding a child.

Ana S.A. Cohen et al.

In a pilot study in rural Kansas, Children’s Mercy’s Genomic Answers for Kids observed 5.5-month less time to diagnosis through the direct-to-provider exome sequencing program compared to the “traditional” primary care provider-referral-to-specialist scheme. In the comparison study, PhenoTips was used to capture patient information and securely annotate clinical features and family history, as well as share de-identified patient data with other rare disease groups for collaborative efforts.

AMERICAN JOURNAL OF HUMAN GENETICS.

MAY 2, 2024

Development and deployment of clinical genome sequencing using a cloud-based platform

Children's Hospital of Eastern Ontario logo, CHEO written in purple.
The Hospital for Sick Children logo with the word "Sick" written in light blue, and "Kids" in dark blue.

Lynette Lau et al.

CHEO and SickKids built and validated an easily updated solution to deliver exome and genome sequencing for Ontarians with a suspected rare disease. PhenoTips was used to link human phenotype ontology (HPO) terms and pedigree information to genomic analysis platforms through.

GENETICS IN MEDICINE.

MAR 16, 2024

Massive Parallel DNA Sequencing of Patients with Inherited Cardiomyopathies in Cyprus and Suggestion of Digenic or Oligogenic Inheritance

Constantina Koutsofti et al.

A systematic study of inherited cardiac conditions in Cyprus applied massive parallel DNA sequencing of 25 families to study inherited cardiomyopathies. All family pedigrees were constructed using PhenoTips software.

MULTIDISCIPLINARY DIGITAL PUBLISHING INSTITUTE.

FEB 28, 2024

Clinical and genetic characterisation of a large Indian congenital myasthenic syndrome cohort

Kiran Polavarapu et al.

The largest cohort to-date of Indian patients with congenital myasthenic syndromes (CMS) was identified and genetically characterized. All phenotypic data were uploaded onto  PhenoTips, using the Human Phenotype Ontology (HPO) to enable standardization and comparability across patients.

BRAIN.

SEPT 18, 2023

Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery

Care for Rare (Care4Rare) Canada logo in blue, green, red, and black.

Kym M. Boycott et al.

PhenoTips supported the collection of computer-readable phenotypic data. In addition, PhenTips facilitated the data transfer first-step entry into the Care4Rare discovery pipeline.

The Care4Rare Consortium used ‘omic technologies to identify the molecular cause of unsolved rare diseases. As a result, they reached 34% diagnostic yield and made significant contributions to rare disease research. This included the implementation of genome-wide sequencing as a publicly funded test for rare disease diagnosis in Canada.

THE AMERICAN JOURNAL OF HUMAN GENETICS.
Nov 3, 2022

The performance of genome sequencing as a first-tier test for neurodevelopmental disorders

Bart P. G. H. van der Sanden et al.

Researchers used PhenoTips to collect HPO-coded phenotypic information from electronic health records. They evaluated diagnostic yield for 150 patients with neurodevelopmental disorders and their parents. This was achieved with genome sequencing and the current standard of care.

Results found similar yield but improved efficiency of genome sequencing as a first-tier test for neurodevelopmental disorders.

THE EUROPEAN JOURNAL OF HUMAN GENETICS.
Sep 16, 2022

Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes

Children's Mercy Kansas City logo in blue next to a blue outline of an adult figure holding a child.

Ana SA Cohen et al.

960 families with suspected genetic disorders received comprehensive diagnostic and candidate analyses through the Genomic Answers for Kids (GA4K) program. PhenoTips was used to store structured phenotypes and prioritize variants and pedigrees.

GENETICS IN MEDICINE.
Mar 16, 2022

Genomics4RD: An integrated platform to share Canadian deep-phenotype and multiomic data for international rare disease gene discovery

Genomics4rd logo, the dot over the I in "genomics" is a blue cloud "Canada's rare disease research platform", in blue and black.

Hannah G. Driver et al.

Genomics4RD is a platform to share Canadian phenotypic and multiomic data, collected and standardized via PhenoTips. The data is shared between researchers to discover the mechanisms that cause rare diseases.

HUMAN MUTATION.
Feb 19, 2022

PhenomeCentral: 7 years of rare disease matchmaking

The Phenome Central logo in dark grey and orange.

Matthew Osmond et al.

Over the past 7 years PhenomeCentral has resulted in 60,000 matches and multiple gene discoveries. PhenomeCentral is a rare disease data repository facilitating matchmaking built on PhenoTips technology.

Read more about where PhenomeCentral is today and its potential future applications.

HUMAN MUTATION.

Feb 14, 2022

Genome Sequencing as a Diagnostic Test in Children With Unexplained Medical Complexity.

The Hospital for Sick Children logo with the word "Sick" written in light blue, and "Kids" in dark blue.

Gregory Costain et al.

PhenoTips was used to capture family history and HPO-coded phenotype data of 138 children with medical complexity. The children who received prior negative genetic testing results received genome sequencing resulting in a new diagnosis for 31% of patients.

JAMA NETWORK OPEN.
Sept 22, 2020

The Cardiac Genome Clinic: implementing genome sequencing in pediatric heart disease.

The Hospital for Sick Children logo with the word "Sick" written in light blue, and "Kids" in dark blue.

Miriam S. Reuter et al.

Genome sequencing data of 111 families with cardiac lesions were analyzed for rare, disease-associated variation. PhenoTips was used to capture HPO-coded phenotype data.

The results demonstrated the diagnostic and scientific value of genome sequencing in pediatric heart disease, anticipating its role as a first-tier diagnostic test.

GENETICS IN MEDICINE.
Feb 10, 2020
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