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Variant Analyst Jobs in Boston, MA (NOW HIRING)

Triveni Bio

Director, AI and Data Science

Watertown, MA · On-site

$240K - $255K/yr

Lead human genetics analyses, including human genetics scoring, variant interpretation, and genotype-phenotype association studies * Drive real-world evidence (RWE) data curation and analysis using ...

New

Triveni Bio

Director, AI and Data Science

Watertown, MA · On-site

$240K - $255K/yr

Lead human genetics analyses, including human genetics scoring, variant interpretation, and genotype-phenotype association studies * Drive real-world evidence (RWE) data curation and analysis using ...

New

Merck Group

Engineer 3

Bedford, MA · On-site

$85K - $149K/yr

Cell counting, metabolite analysis, protein quantification, glycan and charge variant analysis; flow cytometry, PCR, and ELISA experience. * Skilled in statistical analysis, experimental design, and ...

Teledyne

SAP SD Analyst

Billerica, MA

$120K - $160K/yr

Experience with Variant Configuration, Trade Compliance, Customer Repair Process and LTMC/LTMOM preferred. * Translate user's requests into application system solutions. Analyze system user ...

Novartis

Human Genetics Laboratory Leader

Cambridge, MA · On-site

$152K - $283K/yr

The successful candidate will lead a small team of biologists and shape the genotype-to-phenotype translation strategy, integrating rare variant genetics, functional biology, and advanced analytical ...

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All JobsVariant Analyst JobsVariant Analyst Jobs in Boston, MA

Variant Analyst information

See Boston, MA salary details

$33.7K

$79.7K

$141.4K

How much do variant analyst jobs pay per year?

As of Sep 6, 2026, the average yearly pay for variant analyst in Boston, MA is $79,688.00, according to ZipRecruiter salary data. Most workers in this role earn between $57,100.00 and $94,600.00 per year, depending on experience, location, and employer.

What is a variant analyst?

A Variant Analyst is a professional who analyzes genetic variations in DNA sequences to identify mutations associated with diseases or traits. They interpret sequencing data, use bioinformatics tools, and contribute to clinical or research-based genetic analyses. Their work helps in diagnosing genetic disorders, guiding treatment decisions, and advancing precision medicine.

What are the typical daily responsibilities of a variant analyst?

A Variant Analyst typically spends their day analyzing genetic sequencing data to identify, classify, and interpret genetic variants of clinical or research significance. They utilize specialized bioinformatics software to process raw data, review scientific literature for evidence supporting variant classification, and document their findings in detailed reports. Collaboration is common, as analysts often work closely with laboratory geneticists, clinicians, and other members of a multidisciplinary team to ensure accurate and relevant results. Staying updated with the latest guidelines and advances in genomics is also an important part of the role.

What are the key skills and qualifications needed to thrive in the variant analyst position?

To thrive as a Variant Analyst, you need a solid background in genetics or molecular biology, experience in data analysis, and a relevant bachelor's or advanced degree. Familiarity with bioinformatics tools such as Variant Call Format (VCF) analysis software, genomic databases, and proficiency in scripting languages like Python or R is highly valued, as is certification in clinical genetics or genomics. Strong attention to detail, analytical thinking, and effective communication skills distinguish top candidates in this field. These skills and qualities ensure accurate variant interpretation, effective cross-functional collaboration, and meaningful contributions to diagnostics or research.

What are the most commonly searched types of Variant Analyst jobs in Boston, MA?

The most popular types of Variant Analyst jobs in Boston, MA are:

What are popular job titles related to Variant Analyst jobs in Boston, MA?

For Variant Analyst jobs in Boston, MA, the most frequently searched job titles are:

What job categories do people searching Variant Analyst jobs in Boston, MA look for?

The top searched job categories for Variant Analyst jobs in Boston, MA are:

Variant Analyst jobs near you
Infographic showing various Variant Analyst job openings in Boston, MA as of August 2026, with employment types broken down into 93% Full Time, and 7% Part Time. Highlights an 71% In-person, 17% Hybrid, and 12% Remote job distribution, with an average salary of $79,688 per year, or $38.3 per hour.

Associate Director, Bioinformatics

Rhythm Pharmaceuticals

Boston, MA • On-site

Full-time

Re-posted 22 days ago

Job description

Company Overview
Rhythm is a global, commercial-stage biopharmaceutical company committed to transforming the lives of patients living with rare neuroendocrine diseases. We develop medicines for previously untreatable or undertreated diseases. We recognize the courage it takes for patients and their caregivers to begin their journey of advocacy to find the answers they need. Their courage inspires us to challenge convention, ask bold questions and seek answers for them. Every day, we strive for excellence through our willingness to adapt, learn, and our tenacity to overcome barriers, together.
Opportunity Overview
We are seeking a highly motivated Associate Director of Bioinformatics within Rhythm's Research group to support of our clinical, regulatory, and scientific objectives in the rare neuroendocrine/obesity/metabolic disease therapeutic area. The successful candidate will have a strong background in biostatistics and genetics and will be responsible for integrative analyses across the obesity and metabolic disease therapeutic areas. A core focus of this position will be the development and implementation of algorithmic phenotyping approaches using electronic medical records (EMR) and real-world datasets, enabling robust patient stratification, cohort definition, and integration with genomics and biomarker data. This position is ideal for a technically strong investigator who thrives in a fast-paced environment and is motivated to apply and scale high-impact data science infrastructure alongside a growing team.
Responsibilities and Duties
  • Design phenotyping pipelines that leverage EMR/EHR and real-world data to define disease cohorts, endpoints, and longitudinal outcomes.
  • Develop scalable approaches for cohort identification, feature extraction, and phenotype validation, including rule-based and machine learning methods.
  • Maintain high-throughput rare variant curation and classification models.
  • Execute the design, development, and deployment of data analysis pipelines, statistical models, and predictive tools to support genetics-led programs.
  • Lead hands-on integration of clinical, EMR, genomics, and biomarker datasets, enabling multi-modal analyses.
  • Build and maintain reproducible workflows for data ingestion, harmonization (e.g., coding systems, ontologies), QC, and analysis (SQL, Python, R).
  • Apply statistical genetics and advanced analytics to link phenotypic definitions with genetic signals, including rare variant analyses.
  • Drive improvements in data infrastructure and phenotyping frameworks to support team expansion and increased dataset complexity.

Qualifications and Skills
  • Ph.D. in Biostatistics, Neuroscience, Genetics, or related quantitative field.
  • ~5+ years of relevant experience in biotechnology, pharmaceuticals, or healthcare analytics.
  • Experience with neuroendocrine, obesity/metabolic-related biology and datasets.
  • Experience applying machine learning and AI models to real-world and clinical datasets, including model development, evaluation, and deployment in production or near-production settings.
  • Strong hands-on expertise in SQL, Python, and R, with experience building production-quality data pipelines.
  • Experience with variant calling pipelines, variant interpretation and ACMG rare variant classification.
  • Demonstrated experience in EMR/EHR and real-world data analysis (e.g., UK Biobank, All of Us) including cohort building and longitudinal data modeling.
  • Proven track record in algorithmic phenotyping, including use of coding systems (ICD, CPT, SNOMED), clinical ontologies, and feature engineering.
  • Familiarity with broader bioinformatics/multi-omics methodologies including RNA-seq, methylation analysis, long-read sequencing would be advantageous.
  • Strong problem-solving skills and ability to operate independently in a fast-paced, execution-focused environment.
  • Excellent communication skills with the ability to clearly present complex analytical outputs to technical stakeholders.

This role can be remote or based out of our corporate office in Boston, Massachusetts. Rhythm operates in a hybrid-work model. Candidates applying must be willing and able to be in the Boston office in coordination with their department and business needs. This role may involve some travel.
More about Rhythm
We are a dynamic and growing global team spanning more than a dozen countries. At Rhythm we are dedicated to transforming the lives of patients living with rare neuroendocrine diseases by rapidly advancing care and precision medicines that address the root cause. Our team is passionate about expanding access to reach more patients and developing novel therapies for other rare neuroendocrine diseases, including congenital hyperinsulinism. 
At Rhythm our core values are:
  • We are committed to advancing scientific understanding to improve patients’ lives
  • We are inspired to tackle tough challenges and have the courage to ask bold questions
  • We are eager to learn and adapt
  • We believe collaboration and ownership are foundational for our success
  • We value the unique contribution each individual brings to furthering our mission

Inherent in our core values is the commitment to act ethically and with integrity in all we do.
Rhythm is an equal employment opportunity employer and does not discriminate against any applicant because of race, creed, color, age, national origin, ancestry, religion, gender, sexual orientation, disability, genetic information, veteran status, military status, application for military service, or any other class protected by state or federal law.
Headquartered in Boston, Rhythm is proud to have been named one of the Top Places to Work in Massachusetts.
 

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