{"entity": "researcher", "timestamp": "2026-09-23T22:16:52.612Z", "family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "affiliations": ["Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbbf41bd13c347898cc7fa0cedd4e6b2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbbf41bd13c347898cc7fa0cedd4e6b2"}}, "publications": [{"entity": "publication", "iuid": "5e0e17d959554786ad6368f8283e32d2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5e0e17d959554786ad6368f8283e32d2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5e0e17d959554786ad6368f8283e32d2"}}, "title": "High throughput barcoding method for genome-scale phasing.", "authors": [{"family": "Redin", "given": "David", "initials": "D"}, {"family": "Frick", "given": "Tobias", "initials": "T"}, {"family": "Aghelpasand", "given": "Hooman", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbbf41bd13c347898cc7fa0cedd4e6b2.json"}}, {"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2019-12-02", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "18116", "issn-l": "2045-2322"}, "abstract": "The future of human genomics is one that seeks to resolve the entirety of genetic variation through sequencing. The prospect of utilizing genomics for medical purposes require cost-efficient and accurate base calling, long-range haplotyping capability, and reliable calling of structural variants. Short-read sequencing has lead the development towards such a future but has struggled to meet the latter two of these needs. To address this limitation, we developed a technology that preserves the molecular origin of short sequencing reads, with an insignificant increase to sequencing costs. We demonstrate a novel library preparation method for high throughput barcoding of short reads where millions of random barcodes can be used to reconstruct megabase-scale phase blocks.", "doi": "10.1038/s41598-019-54446-x", "pmid": "31792271", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6889410"}, {"db": "pii", "key": "10.1038/s41598-019-54446-x"}], "notes": [], "created": "2026-09-23T10:57:25.414Z", "modified": "2026-09-23T10:57:25.491Z"}, {"entity": "publication", "iuid": "d6f580652dfe41b391918727981fd5c3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d6f580652dfe41b391918727981fd5c3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d6f580652dfe41b391918727981fd5c3"}}, "title": "Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.", "authors": [{"family": "Tiukova", "given": "Ievgeniia A", "initials": "IA", "orcid": "0000-0002-0408-3515", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ba02f5a1b89e4cc5b9e77ad2d6b1ba4b.json"}}, {"family": "Pettersson", "given": "Mats E", "initials": "ME"}, {"family": "Hoeppner", "given": "Marc P", "initials": "MP"}, {"family": "Olsen", "given": "Remi-Andre", "initials": "RA"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbbf41bd13c347898cc7fa0cedd4e6b2.json"}}, {"family": "Nielsen", "given": "Jens", "initials": "J"}, {"family": "Dainat", "given": "Jacques", "initials": "J"}, {"family": "Lantz", "given": "Henrik", "initials": "H"}, {"family": "S\u00f6derberg", "given": "Jonas", "initials": "J"}, {"family": "Passoth", "given": "Volkmar", "initials": "V"}], "type": "journal article", "published": "2019-05-01", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "14", "issue": "5", "pages": "e0215077", "issn-l": "1932-6203"}, "abstract": "Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.", "doi": "10.1371/journal.pone.0215077", "pmid": "31042716", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6493715"}, {"db": "pii", "key": "PONE-D-18-32895"}], "notes": [], "created": "2026-09-23T12:40:57.189Z", "modified": "2026-09-23T12:40:57.311Z"}, {"entity": "publication", "iuid": "ae099c48ae1a48d3b15f364265c1c073", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ae099c48ae1a48d3b15f364265c1c073.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ae099c48ae1a48d3b15f364265c1c073"}}, "title": "Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.", "authors": [{"family": "Eisfeldt", "given": "Jesper", "initials": "J"}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12ccdc228a31454b8d43136e9708350b.json"}}, {"family": "Vezzi", "given": "Francesco", "initials": "F", "orcid": "0000-0002-0243-0018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ec1f9d0b4a524885b29fb96600d879f7.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbbf41bd13c347898cc7fa0cedd4e6b2.json"}}, {"family": "Gruselius", "given": "Joel", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e071495ddf43e5b570dfb22c1fec06.json"}}, {"family": "Syk Lundberg", "given": "Elisabeth", "initials": "E"}, {"family": "Carvalho", "given": "Claudia M B", "initials": "CMB", "orcid": "0000-0002-2090-298X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/957f6ddd88b24cf3aee597cf2095ec56.json"}}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d28fb4cc61f4033b2ac525fed3d6b94.json"}}], "type": "journal article", "published": "2019-02-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "15", "issue": "2", "pages": "e1007858", "issn-l": "1553-7390"}, "abstract": "Complex chromosomal rearrangements (CCRs) are rearrangements involving more than two chromosomes or more than two breakpoints. Whole genome sequencing (WGS) allows for outstanding high resolution characterization on the nucleotide level in unique sequences of such rearrangements, but problems remain for mapping breakpoints in repetitive regions of the genome, which are known to be prone to rearrangements. Hence, multiple complementary WGS experiments are sometimes needed to solve the structures of CCRs. We have studied three individuals with CCRs: Case 1 and Case 2 presented with de novo karyotypically balanced, complex interchromosomal rearrangements (46,XX,t(2;8;15)(q35;q24.1;q22) and 46,XY,t(1;10;5)(q32;p12;q31)), and Case 3 presented with a de novo, extremely complex intrachromosomal rearrangement on chromosome 1. Molecular cytogenetic investigation revealed cryptic deletions in the breakpoints of chromosome 2 and 8 in Case 1, and on chromosome 10 in Case 2, explaining their clinical symptoms. In Case 3, 26 breakpoints were identified using WGS, disrupting five known disease genes. All rearrangements were subsequently analyzed using optical maps, linked-read WGS, and short-read WGS. In conclusion, we present a case series of three unique de novo CCRs where we by combining the results from the different technologies fully solved the structure of each rearrangement. The power in combining short-read WGS with long-molecule sequencing or optical mapping in these unique de novo CCRs in a clinical setting is demonstrated.", "doi": "10.1371/journal.pgen.1007858", "pmid": "30735495", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6368290"}, {"db": "pii", "key": "PGENETICS-D-18-00854"}], "notes": [], "created": "2026-09-23T09:25:53.119Z", "modified": "2026-09-23T09:25:53.290Z"}, {"entity": "publication", "iuid": "1a88e2addd034774a2b5504620603776", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1a88e2addd034774a2b5504620603776.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1a88e2addd034774a2b5504620603776"}}, "title": "Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.", "authors": [{"family": "Nazaryan-Petersen", "given": "Lusine", "initials": "L"}, {"family": "Eisfeldt", "given": "Jesper", "initials": "J", "orcid": "0000-0003-3716-4917", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83d05cbf798f4b48800dc89b57427cf2.json"}}, {"family": "Pettersson", "given": "Maria", "initials": "M", "orcid": "0000-0003-3120-1625", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12ccdc228a31454b8d43136e9708350b.json"}}, {"family": "Lundin", "given": "Johanna", "initials": "J"}, {"family": "Nilsson", "given": "Daniel", "initials": "D", "orcid": "0000-0001-5831-385X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49e071495ddf43e5b570dfb22c1fec06.json"}}, {"family": "Wincent", "given": "Josephine", "initials": "J"}, {"family": "Lieden", "given": "Agne", "initials": "A"}, {"family": "Lovmar", "given": "Lovisa", "initials": "L"}, {"family": "Ottosson", "given": "Jesper", "initials": "J"}, {"family": "Gacic", "given": "Jelena", "initials": "J", "orcid": "0000-0002-1431-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e03050cfc6704c5dbf78a8b4fc5bf643.json"}}, {"family": "M\u00e4kitie", "given": "Outi", "initials": "O", "orcid": "0000-0002-4547-001X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/79b7b7154e694a85b1498dd78fe370c0.json"}}, {"family": "Nordgren", "given": "Ann", "initials": "A"}, {"family": "Vezzi", "given": "Francesco", "initials": "F"}, {"family": "Wirta", "given": "Valtteri", "initials": "V", "orcid": "0000-0003-3811-5439", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a4f538e838c483eb968174f2df89165.json"}}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbbf41bd13c347898cc7fa0cedd4e6b2.json"}}, {"family": "Hjortsh\u00f8j", "given": "Tina Duelund", "initials": "TD"}, {"family": "Jespersgaard", "given": "Cathrine", "initials": "C"}, {"family": "Houssari", "given": "Rayan", "initials": "R"}, {"family": "Pignata", "given": "Laura", "initials": "L"}, {"family": "Bak", "given": "Mads", "initials": "M"}, {"family": "Tommerup", "given": "Niels", "initials": "N", "orcid": "0000-0003-2304-0112", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9012926182034ede9651bb6452421589.json"}}, {"family": "Lundberg", "given": "Elisabeth Syk", "initials": "ES", "orcid": "0000-0001-5692-725X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/750ccc78742d4905919329226545f20d.json"}}, {"family": "T\u00fcmer", "given": "Zeynep", "initials": "Z"}, {"family": "Lindstrand", "given": "Anna", "initials": "A", "orcid": "0000-0003-0806-5602", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3d28fb4cc61f4033b2ac525fed3d6b94.json"}}], "type": "journal article", "published": "2018-11-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "14", "issue": "11", "pages": "e1007780", "issn-l": "1553-7390"}, "abstract": "Clustered copy number variants (CNVs) as detected by chromosomal microarray analysis (CMA) are often reported as germline chromothripsis. However, such cases might need further investigations by massive parallel whole genome sequencing (WGS) in order to accurately define the underlying complex rearrangement, predict the occurrence mechanisms and identify additional complexities. Here, we utilized WGS to delineate the rearrangement structure of 21 clustered CNV carriers first investigated by CMA and identified a total of 83 breakpoint junctions (BPJs). The rearrangements were further sub-classified depending on the patterns observed: I) Cases with only deletions (n = 8) often had additional structural rearrangements, such as insertions and inversions typical to chromothripsis; II) cases with only duplications (n = 7) or III) combinations of deletions and duplications (n = 6) demonstrated mostly interspersed duplications and BPJs enriched with microhomology. In two cases the rearrangement mutational signatures indicated both a breakage-fusion-bridge cycle process and haltered formation of a ring chromosome. Finally, we observed two cases with Alu- and LINE-mediated rearrangements as well as two unrelated individuals with seemingly identical clustered CNVs on 2p25.3, possibly a rare European founder rearrangement. In conclusion, through detailed characterization of the derivative chromosomes we show that multiple mechanisms are likely involved in the formation of clustered CNVs and add further evidence for chromoanagenesis mechanisms in both \"simple\" and highly complex chromosomal rearrangements. Finally, WGS characterization adds positional information, important for a correct clinical interpretation and deciphering mechanisms involved in the formation of these rearrangements.", "doi": "10.1371/journal.pgen.1007780", "pmid": "30419018", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6258378"}, {"db": "pii", "key": "PGENETICS-D-18-01290"}], "notes": [], "created": "2026-09-23T09:45:48.929Z", "modified": "2026-09-23T10:20:02.414Z"}]}