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Merged
shilpigoeldev merged 13 commits into from
Mar 24, 2025
Merged

Feature/ndrs2 2031/sheffield brca regex updates #146

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1bdb6ef
updates to sheffield regex
lauramccluskey1 Jan 15, 2025
fd38fc9
update mistake in panel
lauramccluskey1 Jan 27, 2025
f6a51bc
Update panels
lauramccluskey1 Feb 12, 2025
bf7b9d5
tidy code
lauramccluskey1 Feb 13, 2025
270a1dc
tidy code
lauramccluskey1 Feb 13, 2025
b42a1b6
update to gene list and tidying
lauramccluskey1 Feb 19, 2025
1339e15
update cdna and protein regex
lauramccluskey1 Feb 19, 2025
36327df
update cdna regex and unittests
lauramccluskey1 Feb 20, 2025
7753c53
Merge branch 'develop' into feature/NDRS2-2031/sheffield_brca_regex_u…
ollietulloch Feb 20, 2025
6e74a9b
updates from code review
lauramccluskey1 Mar 7, 2025
f983c74
updates from code review
lauramccluskey1 Mar 7, 2025
65c94c7
Removed brackets from protein capture in tests
shilpigoeldev Mar 18, 2025
9a77743
Merge branch 'develop' into feature/NDRS2-2031/sheffield_brca_regex_u…
shilpigoeldev Mar 18, 2025
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132 changes: 95 additions & 37 deletions lib/import/brca/providers/sheffield/sheffield_handler.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -13,14 +13,14 @@ def process_fields(record)
geno = record.raw_fields['genetictestscope']
return if NON_BRCA_SCOPE.include?(geno)

@genes_set = []
genotype = Import::Brca::Core::GenotypeBrca.new(record)
genotype.add_passthrough_fields(record.mapped_fields,
record.raw_fields,
PASS_THROUGH_FIELDS)
add_test_type(genotype, record)
add_organisationcode_testresult(genotype)
add_test_scope_from_geno_karyo(genotype, record)

res = process_variants_from_record(genotype, record)
res.map { |cur_genotype| @persister.integrate_and_store(cur_genotype) }
end
Expand All @@ -34,37 +34,46 @@ def add_test_scope_from_geno_karyo(genotype, record)
karyo = record.raw_fields['karyotypingmethod'].strip
process_method = GENETICTESTSCOPE_METHOD_MAPPING[genotype_str]
if process_method
send(process_method, karyo, genotype)
send(process_method, karyo, genotype, record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_familial_mutation(karyo, genotype)
if BRCA_FAMILIAL_GENE_MAPPING.keys.include? karyo
def process_scope_familial_mutation(karyo, genotype, record)
if BRCA_FAMILIAL_GENE_MAPPING.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = BRCA_FAMILIAL_GENE_MAPPING[karyo]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_gene_analysis(karyo, genotype)
def process_scope_gene_analysis(karyo, genotype, record)
if BRCA_ANALYSIS_GENE_MAPPING_FS.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
genotype.add_test_scope(:full_screen)
@genes_set = BRCA_ANALYSIS_GENE_MAPPING_FS[karyo]
elsif BRCA_ANALYSIS_GENE_MAPPING_TAR.keys.include? karyo
elsif BRCA_ANALYSIS_GENE_MAPPING_TAR.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = BRCA_ANALYSIS_GENE_MAPPING_TAR[karyo]
get_genes_set_targeted(record)

else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_ovarian_panel(karyo, genotype)
def get_genes_set_targeted(record)
karyo_column = record.raw_fields['karyotypingmethod'].strip
genotype_column = record.raw_fields['genotype'].strip
@genes_set = []
@genes_set.append(karyo_column.scan(BRCA_REGEX))
@genes_set.append(genotype_column.scan(BRCA_REGEX))
end

def process_scope_ovarian_panel(karyo, genotype, _record)
if OVRN_CNCR_PNL_GENE_MAPPING.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN for: #{karyo}"
genotype.add_test_scope(:full_screen)
Expand All @@ -74,7 +83,7 @@ def process_scope_ovarian_panel(karyo, genotype)
end
end

def process_scope_colo_ovarian_panel(karyo, genotype)
def process_scope_colo_ovarian_panel(karyo, genotype, _record)
if OVRN_COLO_PNL_GENE_MAPPING.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN for: #{karyo}"
genotype.add_test_scope(:full_screen)
Expand All @@ -84,78 +93,124 @@ def process_scope_colo_ovarian_panel(karyo, genotype)
end
end

def process_scope_r205(karyo, genotype)
def process_scope_r205(karyo, genotype, record)
if R205_GENE_MAPPING_FS.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
genotype.add_test_scope(:full_screen)
@genes_set = R205_GENE_MAPPING_FS[karyo]
elsif R205_GENE_MAPPING_TAR.keys.include? karyo
elsif R205_GENE_MAPPING_TAR.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = R205_GENE_MAPPING_TAR[karyo]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r206(karyo, genotype)
def process_scope_r206(karyo, genotype, record)
if R206_GENE_MAPPING.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
genotype.add_test_scope(:full_screen)
@genes_set = R206_GENE_MAPPING[karyo]
elsif ['R242.1 :: Predictive testing'].include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = %w[ATM BRCA1 BRCA2 BRIP1 CDH1 CHEK2 EPCAM MLH1 MSH2 MSH6 PALB2 PTEN
RAD51C RAD51D STK11 TP53 PMS2]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r207(karyo, genotype)
def process_scope_r207(karyo, genotype, record)
if R207_GENE_MAPPING_FS.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
genotype.add_test_scope(:full_screen)
@genes_set = R207_GENE_MAPPING_FS[karyo]
elsif R207_GENE_MAPPING_TAR.keys.include? karyo
elsif R207_GENE_MAPPING_TAR.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = R207_GENE_MAPPING_TAR[karyo]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r208(karyo, genotype)
def process_scope_r208(karyo, genotype, record)
if R208_GENE_MAPPING_FS.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
genotype.add_test_scope(:full_screen)
@genes_set = R208_GENE_MAPPING_FS[karyo]
elsif R208_GENE_MAPPING_TAR.keys.include? karyo
elsif R208_GENE_MAPPING_TAR.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = R208_GENE_MAPPING_TAR[karyo]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r208_new(karyo, genotype, record)
genotype_str = record.raw_fields['genotype'].to_s
genotype_genes = genotype_str.scan(BRCA_REGEX).flatten.uniq
if R208_GENE_MAPPING_FS_NEW.keys.include? karyo
@logger.debug "ADDED FULL_SCREEN TEST for: #{karyo}"
genotype.add_test_scope(:full_screen)
@genes_set = R208_GENE_MAPPING_FS_NEW[karyo].dup
# add genes from genotype column
@genes_set.concat(genotype_genes)
if karyo.match(/R208\.1\s::\sNGS\sin\sLeeds/)
date = DateTime.parse(record.raw_fields['authoriseddate'])
@genes_set.concat(%w[RAD51C RAD51D]) if date >= DateTime.parse('01/02/2023')
end
elsif R208_GENE_MAPPING_TAR_NEW.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
@genes_set = @genes_set.uniq
end

def process_scope_r430(karyo, genotype, _record)
if R430_GENE_MAPPING_FS.keys.include? karyo
@genes_set = R430_GENE_MAPPING_FS[karyo]
genotype.add_test_scope(:full_screen)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r240(karyo, genotype)
if R240_GENE_MAPPING_TAR.keys.include? karyo
def process_scope_r444(karyo, genotype, _record)
if karyo.match(/R444\.1\s::\sPARPi\sfor\sBreast\scancer.*NGS\sin\sLeeds/)
karyo = 'R444.1 :: PARPi for Breast cancer - NGS in Leeds'
end
if karyo.match(/R444\.2\s::\sPARPi\sfor\sProstate\sCancer.*NGS\sin\sLeeds\ssend\sDNA\sto\sLeeds/)
karyo = 'R444.2 :: PARPi for Prostate Cancer - NGS in Leeds send DNA to Leeds'
end
if R444_GENE_MAPPING.keys.include? karyo
@genes_set = R444_GENE_MAPPING[karyo]
genotype.add_test_scope(:full_screen)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r240(karyo, genotype, record)
if R240_GENE_MAPPING_TAR.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = R240_GENE_MAPPING_TAR[karyo]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
end

def process_scope_r242(karyo, genotype)
if R242_GENE_MAPPING_TAR.keys.include? karyo
def process_scope_r242(karyo, genotype, record)
if R242_GENE_MAPPING_TAR.include? karyo
@logger.debug "ADDED TARGETED TEST for: #{karyo}"
genotype.add_test_scope(:targeted_mutation)
@genes_set = R242_GENE_MAPPING_TAR[karyo]
get_genes_set_targeted(record)
else
genotype.add_test_scope(:no_genetictestscope)
end
Expand Down Expand Up @@ -294,15 +349,18 @@ def add_other_genes_with_status(other_genes, genotype, genotypes, status)
end

def process_multi_genes(genotype, record, genotypes)
positive_genes = record.raw_fields['genotype'].scan(BRCA_REGEX).flatten.uniq
raw_genotypes = record.raw_fields['genotype'].split(positive_genes[-1])
raw_genotypes[1].prepend(positive_genes[-1])
positive_genes = record.raw_fields['genotype'].scan(BRCA_REGEX).flatten
positive_genes = positive_genes.join('|')
raw_genotypes = record.raw_fields['genotype'].split(/(?=#{positive_genes})/)

process_raw_genotypes(raw_genotypes, genotype, genotypes)
end

def process_raw_genotypes(raw_genotypes, genotype, genotypes)
raw_genotypes.each do |raw_genotype|
raw_genotype.scan(BRCA_REGEX)
next if raw_genotype.scan(BRCA_REGEX).empty?

genotype_dup = genotype.dup
genotype_dup.add_gene($LAST_MATCH_INFO[:brca]&.upcase)
if positive_cdna?(raw_genotype) || positive_exonvariant?(raw_genotype)
Expand Down Expand Up @@ -339,8 +397,8 @@ def process_fullscreen_records(genotype, record, genotypes)
process_failed_full_screen(genotype, record, genotypes)
elsif positive_cdna?(genotype_str) || positive_exonvariant?(genotype_str)
process_variant_fs_records(genotype, record, genotypes)
elsif only_protein_impact?(record) ||
genotype_str.scan(/see\sbelow|comments/ix).size.positive?
else
# else give a test status of 4 (unknown)
add_other_genes_with_status(@genes_set, genotype, genotypes, 4)
end
genotypes
Expand All @@ -360,7 +418,7 @@ def process_multiple_variant_fs_record(genotype, record, genotypes)
if positive_genes.blank?
add_other_genes_with_status(@genes_set, genotype, genotypes, 4)
elsif positive_genes.size > 1
process_multi_genes(genotype, record, genotypes)
genotypes = process_multi_genes(genotype, record, genotypes)
else
process_positive_record(genotype, record, genotypes, positive_genes)
end
Expand Down Expand Up @@ -482,16 +540,16 @@ def get_cdna_mutation(raw_genotype)
def get_gene(record)
genotype_str = record.raw_fields['genotype'].to_s
positive_genes = genotype_str.scan(BRCA_REGEX).flatten.uniq
if positive_genes.size.zero?
if positive_genes.empty?
positive_genes = record.raw_fields['karyotypingmethod'].scan(BRCA_REGEX).flatten.uniq
end
positive_genes
end

def only_protein_impact?(record)
variant = record.raw_fields['genotype']
variant.scan(CDNA_REGEX).size.zero? &&
variant.scan(EXON_VARIANT_REGEX).size.zero? &&
variant.scan(CDNA_REGEX).empty? &&
variant.scan(EXON_VARIANT_REGEX).empty? &&
variant.scan(PROTEIN_REGEX).size.positive?
end

Expand Down
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