Summer Intern - Evaluating Genetic Sequencing Approaches

Livestock Improvement Corporation (LIC); Hamilton; On-site; NZD 12,357,000 - 16,476,000; Full time

Benefits offered by this job

Paid internship

Job summary

Livestock Improvement Corporation (LIC) invites applications for a paid summer internship in its R&D group. The project focuses on evaluating long-read sequencing approaches (ONT and PacBio) for structural variant discovery in dairy cattle, using multiple tissue types.

The role includes analyzing sequencing quality metrics, performing SV discovery, and comparing with SNP-array data to guide future sequencing strategies.

Qualifications

• Undergraduate experience in molecular genetics
• Command line/HPC experience
• We particularly encourage genetics or data science students to apply

Responsibilities

• Assess and compare quality of long-read sequencing data from ONT and PacBio across ear tissue, blood, and semen.
• Perform structural variant discovery using long-read data and compare with short-read data from the same animals.
• Investigate concordance between sequencing-based variants and SNP-array inferences.

Skills

Molecular genetics

Command line

HPC

Education

NZQA levels 6-10

Tools

HPC

Job description

LIC’s Research and Development (R&D) group is driving innovation to keep New Zealand farmers and their businesses at the forefront of the global dairy industry. Our world-class team is actively engaged in cutting-edge work across genetics, genomics, reproduction, animal health, statistics, and machine learning.

In partnership with the Ministry of Business, Innovation and Employment, we’re offering summer internships that provide hands‑on experience across a diverse range of scientific and technical areas—from genetic analysis to data science and modelling—leveraging both in‑house and cloud‑based computing platform

Title

Project Details:

Evaluating different sequencing approaches for structural variant discovery.

Project Scope

Livestock Improvement Corporation (LIC) is undertaking a range of research initiatives aimed at identifying and managing large‑effect genetic variants in dairy cattle populations. One important class of these variants is de novo mutations—genetic changes that arise spontaneously in an individual rather than being inherited from its parents. While most de novo mutations have little or no biological impact, some can influence health, fertility, productivity, or other economically important traits. Structural variants—including large insertions, deletions, inversions, and translocations—represent some of the most impactful forms of genetic variation due to their potential to affect large regions of the genome. However, these variants have historically been difficult to detect using traditional short‑read sequencing technologies. Recent advances in long‑read sequencing provide new opportunities to accurately identify and characterise structural variation and improve our understanding of genomic diversity in dairy cattle. LIC has generated a long‑read sequence dataset using both Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) platforms across multiple biological sample types, including ear tissue, blood, and semen. The successful student will contribute to evaluating the quality and performance of these sequencing approaches and tissue sources for structural variant discovery. The findings will help guide future sequencing strategies and support LIC's ongoing efforts to improve the detection and management of novel genetic variation in New Zealand dairy cattle populations.

Your Contribution

The successful student will contribute to the project by assessing and comparing the quality of long read sequencing data generated using Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) platforms across multiple sample types, including ear tissue samples, blood, and semen. They will generate and analyse sequencing quality metrics to evaluate the suitability of different sequencing technologies and tissue sources for downstream genomic analyses. In addition, the student will perform structural variant discovery using long‑read sequence data and compare the resulting variant calls with those obtained from short‑read sequencing data generated from the same animals. They will also investigate the concordance and discrepancies between variants identified through sequencing approaches and those inferred from SNP array data. Through these analyses, the student will gain experience in genomic data analysis while contributing valuable insights into the optimal strategies for structural variant detection in dairy cattle.

Expected Outputs

The outcomes of this project will directly inform LIC’s future strategy for de novo structural variant discovery by identifying the most suitable tissue types and long‑read sequencing technologies for generating high‑quality genomic data. This will support more cost‑effective and targeted investment in future sequencing initiatives. The project will also provide valuable insights into the additional information that long‑read sequencing can deliver compared with existing short‑read sequencing and SNP‑chip approaches, particularly for the detection of structural variants. These findings will help LIC evaluate the value of incorporating long‑read sequencing into routine research and development workflows and strengthen our ability to identify and manage novel genetic variation within the NZ dairy cattle population.

Key Skills Required

• Undergraduate experience in molecular genetics
• Command line/HPC experience
• We particularly encourage genetics or data science students to apply

To Be Eligible For These Internships Students Must Be

• Legally permitted to work in New Zealand.
• Studying, or have studied, an undergraduate or postgraduate qualification at NZQA level 6-10 If study has been completed, the final semester should have ended within the last 12 months.
• Studying, or have studied, science, technology, engineering, design or business at a New Zealand tertiary education institute.
• Be able to work on‑site at our Head Office in Newstead Hamilton for the duration of the internship

Application Information

If you have worked for LIC before, you can still apply if:

• your job was part‑time or temporary
• you only held one R&D Experience Grant internship with LIC.

Please attach an up‑to‑date CV and your academic transcript with your application.

The internship is a paid opportunity offering $29.90 per hour for a period of 10 weeks. You will be required to work a minimum of 30 hours per week, up to a maximum of 400 hours to be completed by 31 March 2027. Participation in the project will be based physically at LIC. At the conclusion of the internship, you will be required to deliver a presentation and submit a report.

Applications close: 13th September 2026 or earlier if the roles are filled.